3HZN | pdb_00003hzn

Structure of the Salmonella typhimurium nfnB dihydropteridine reductase

PDB DOI: https://doi.org/10.2210/pdb3HZN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-23 Released: 2009-07-07
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Skarina, T., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.222 (Depositor), 0.219 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the Salmonella typhimurium nfnB dihydropteridine reductase

Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Skarina, T., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 205.58 kDa
Atom Count: 15,104
Modelled Residue Count: 1,751
Deposited Residue Count: 1,760
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-insensitive NAD(P)H nitroreductase	A, B, C, D, E A, B, C, D, E, F, G, H	220	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: nfnB, nfsI, STM0578 EC: 1
UniProt
Find proteins for P15888 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P15888 Go to UniProtKB: P15888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15888
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain WB [auth F] MOL2 format, chain U [auth B] MOL2 format, chain WB [auth F] mmCIF format, chain U [auth B] mmCIF format, chain WB [auth F]	U [auth B], WB [auth F]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain U [auth B] Focus chain WB [auth F] Interactions & Density Focus chain U [auth B] Focus chain WB [auth F]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain NC [auth H] SDF format, chain V [auth B] SDF format, chain XB [auth F] SDF format, chain ZA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain NC [auth H] MOL2 format, chain V [auth B] MOL2 format, chain XB [auth F] MOL2 format, chain ZA [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain NC [auth H] mmCIF format, chain V [auth B] mmCIF format, chain XB [auth F] mmCIF format, chain ZA [auth D]	EA [auth C] FA [auth C] I [auth A] NC [auth H] V [auth B] EA [auth C], FA [auth C], I [auth A], NC [auth H], V [auth B], XB [auth F], ZA [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain NC [auth H] Focus chain V [auth B] Focus chain XB [auth F] Focus chain ZA [auth D] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain NC [auth H] Focus chain V [auth B] Focus chain XB [auth F] Focus chain ZA [auth D]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain AC [auth F] SDF format, chain BB [auth D] SDF format, chain BC [auth F] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain EC [auth G] SDF format, chain FB [auth D] SDF format, chain FC [auth G] SDF format, chain GA [auth C] SDF format, chain GB [auth D] SDF format, chain GC [auth G] SDF format, chain HA [auth C] SDF format, chain HC [auth G] SDF format, chain IA [auth C] SDF format, chain IC [auth G] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain NB [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain OB [auth E] SDF format, chain OC [auth H] SDF format, chain PB [auth E] SDF format, chain PC [auth H] SDF format, chain QB [auth E] SDF format, chain QC [auth H] SDF format, chain RB [auth E] SDF format, chain RC [auth H] SDF format, chain SC [auth H] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YB [auth F] SDF format, chain ZB [auth F] MOL2 format, chain AB [auth D] MOL2 format, chain AC [auth F] MOL2 format, chain BB [auth D] MOL2 format, chain BC [auth F] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain EC [auth G] MOL2 format, chain FB [auth D] MOL2 format, chain FC [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth D] MOL2 format, chain GC [auth G] MOL2 format, chain HA [auth C] MOL2 format, chain HC [auth G] MOL2 format, chain IA [auth C] MOL2 format, chain IC [auth G] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth E] MOL2 format, chain OC [auth H] MOL2 format, chain PB [auth E] MOL2 format, chain PC [auth H] MOL2 format, chain QB [auth E] MOL2 format, chain QC [auth H] MOL2 format, chain RB [auth E] MOL2 format, chain RC [auth H] MOL2 format, chain SC [auth H] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth F] MOL2 format, chain ZB [auth F] mmCIF format, chain AB [auth D] mmCIF format, chain AC [auth F] mmCIF format, chain BB [auth D] mmCIF format, chain BC [auth F] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain EC [auth G] mmCIF format, chain FB [auth D] mmCIF format, chain FC [auth G] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth D] mmCIF format, chain GC [auth G] mmCIF format, chain HA [auth C] mmCIF format, chain HC [auth G] mmCIF format, chain IA [auth C] mmCIF format, chain IC [auth G] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth E] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain OB [auth E] mmCIF format, chain OC [auth H] mmCIF format, chain PB [auth E] mmCIF format, chain PC [auth H] mmCIF format, chain QB [auth E] mmCIF format, chain QC [auth H] mmCIF format, chain RB [auth E] mmCIF format, chain RC [auth H] mmCIF format, chain SC [auth H] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth F] mmCIF format, chain ZB [auth F]	AB [auth D] AC [auth F] BB [auth D] BC [auth F] CB [auth D] AB [auth D], AC [auth F], BB [auth D], BC [auth F], CB [auth D], DB [auth D], EB [auth D], EC [auth G], FB [auth D], FC [auth G], GA [auth C], GB [auth D], GC [auth G], HA [auth C], HC [auth G], IA [auth C], IC [auth G], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], NB [auth E], O [auth A], OA [auth C], OB [auth E], OC [auth H], PB [auth E], PC [auth H], QB [auth E], QC [auth H], RB [auth E], RC [auth H], SC [auth H], W [auth B], X [auth B], Y [auth B], YB [auth F], ZB [auth F]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain EC [auth G] Focus chain FB [auth D] Focus chain FC [auth G] Focus chain GA [auth C] Focus chain GB [auth D] Focus chain GC [auth G] Focus chain HA [auth C] Focus chain HC [auth G] Focus chain IA [auth C] Focus chain IC [auth G] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain OC [auth H] Focus chain PB [auth E] Focus chain PC [auth H] Focus chain QB [auth E] Focus chain QC [auth H] Focus chain RB [auth E] Focus chain RC [auth H] Focus chain SC [auth H] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YB [auth F] Focus chain ZB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain EC [auth G] Focus chain FB [auth D] Focus chain FC [auth G] Focus chain GA [auth C] Focus chain GB [auth D] Focus chain GC [auth G] Focus chain HA [auth C] Focus chain HC [auth G] Focus chain IA [auth C] Focus chain IC [auth G] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain OC [auth H] Focus chain PB [auth E] Focus chain PC [auth H] Focus chain QB [auth E] Focus chain QC [auth H] Focus chain RB [auth E] Focus chain RC [auth H] Focus chain SC [auth H] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YB [auth F] Focus chain ZB [auth F]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CC [auth F] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain JB [auth D] SDF format, chain JC [auth G] SDF format, chain KC [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain SB [auth E] SDF format, chain TC [auth H] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CC [auth F] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth G] MOL2 format, chain KC [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth E] MOL2 format, chain TC [auth H] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CC [auth F] mmCIF format, chain HB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain JB [auth D] mmCIF format, chain JC [auth G] mmCIF format, chain KC [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth E] mmCIF format, chain TC [auth H] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CC [auth F] HB [auth D] IB [auth D] AA [auth B], BA [auth B], CC [auth F], HB [auth D], IB [auth D], JB [auth D], JC [auth G], KC [auth G], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], SB [auth E], TC [auth H], Z [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CC [auth F] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain JC [auth G] Focus chain KC [auth G] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain TC [auth H] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CC [auth F] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain JC [auth G] Focus chain KC [auth G] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain TC [auth H] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain KB [auth D] SDF format, chain LC [auth G] SDF format, chain TA [auth C] MOL2 format, chain KB [auth D] MOL2 format, chain LC [auth G] MOL2 format, chain TA [auth C] mmCIF format, chain KB [auth D] mmCIF format, chain LC [auth G] mmCIF format, chain TA [auth C]	KB [auth D], LC [auth G], TA [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain KB [auth D] Focus chain LC [auth G] Focus chain TA [auth C] Interactions & Density Focus chain KB [auth D] Focus chain LC [auth G] Focus chain TA [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DC [auth F] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain MC [auth G] SDF format, chain T [auth A] SDF format, chain TB [auth E] SDF format, chain UA [auth C] SDF format, chain UB [auth E] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DC [auth F] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain MC [auth G] MOL2 format, chain T [auth A] MOL2 format, chain TB [auth E] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth E] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain DC [auth F] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain MC [auth G] mmCIF format, chain T [auth A] mmCIF format, chain TB [auth E] mmCIF format, chain UA [auth C] mmCIF format, chain UB [auth E] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C]	CA [auth B] DC [auth F] LB [auth D] MB [auth D] MC [auth G] CA [auth B], DC [auth F], LB [auth D], MB [auth D], MC [auth G], T [auth A], TB [auth E], UA [auth C], UB [auth E], VA [auth C], WA [auth C], XA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain DC [auth F] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain MC [auth G] Focus chain T [auth A] Focus chain TB [auth E] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DC [auth F] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain MC [auth G] Focus chain T [auth A] Focus chain TB [auth E] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain UC [auth H] SDF format, chain VB [auth E] SDF format, chain YA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain UC [auth H] MOL2 format, chain VB [auth E] MOL2 format, chain YA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain UC [auth H] mmCIF format, chain VB [auth E] mmCIF format, chain YA [auth C]	DA [auth B], UC [auth H], VB [auth E], YA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain UC [auth H] Focus chain VB [auth E] Focus chain YA [auth C] Interactions & Density Focus chain DA [auth B] Focus chain UC [auth H] Focus chain VB [auth E] Focus chain YA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.222 (Depositor), 0.219 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.179 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33hzn

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 280.34	α = 90
b = 96.76	β = 90.36
c = 131.84	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary