3LUB | pdb_00003lub

Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LUB/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-17 Released: 2010-03-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.193 (Depositor), 0.197 (DCC)
R-Value Work:
0.151 (Depositor), 0.158 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 345.66 kDa
Atom Count: 26,160
Modeled Residue Count: 3,037
Deposited Residue Count: 3,048
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative creatinine amidohydrolase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	254	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF1877
UniProt
Find proteins for Q5LE76 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LE76 Go to UniProtKB: Q5LE76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LE76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth I] SDF format, chain BA [auth D] SDF format, chain BB [auth I] SDF format, chain FB [auth J] SDF format, chain GB [auth J] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain KB [auth K] SDF format, chain LB [auth K] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain PB [auth L] SDF format, chain Q [auth B] SDF format, chain QB [auth L] SDF format, chain R [auth B] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain XA [auth H] SDF format, chain YA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain FB [auth J] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain KB [auth K] MOL2 format, chain LB [auth K] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain PB [auth L] MOL2 format, chain Q [auth B] MOL2 format, chain QB [auth L] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain YA [auth H] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain FB [auth J] mmCIF format, chain GB [auth J] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain KB [auth K] mmCIF format, chain LB [auth K] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain PB [auth L] mmCIF format, chain Q [auth B] mmCIF format, chain QB [auth L] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain YA [auth H]	AA [auth D] AB [auth I] BA [auth D] BB [auth I] FB [auth J] AA [auth D], AB [auth I], BA [auth D], BB [auth I], FB [auth J], GB [auth J], HA [auth E], IA [auth E], KB [auth K], LB [auth K], M [auth A], N [auth A], OA [auth F], PA [auth F], PB [auth L], Q [auth B], QB [auth L], R [auth B], SA [auth G], TA [auth G], U [auth C], V [auth C], XA [auth H], YA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain FB [auth J] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain KB [auth K] Focus chain LB [auth K] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth L] Focus chain Q [auth B] Focus chain QB [auth L] Focus chain R [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain V [auth C] Focus chain XA [auth H] Focus chain YA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain FB [auth J] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain KB [auth K] Focus chain LB [auth K] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth L] Focus chain Q [auth B] Focus chain QB [auth L] Focus chain R [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain V [auth C] Focus chain XA [auth H] Focus chain YA [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain IB [auth J] SDF format, chain LA [auth E] SDF format, chain MB [auth K] SDF format, chain NB [auth K] SDF format, chain S [auth B] SDF format, chain SB [auth L] SDF format, chain VA [auth G] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain IB [auth J] MOL2 format, chain LA [auth E] MOL2 format, chain MB [auth K] MOL2 format, chain NB [auth K] MOL2 format, chain S [auth B] MOL2 format, chain SB [auth L] MOL2 format, chain VA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain IB [auth J] mmCIF format, chain LA [auth E] mmCIF format, chain MB [auth K] mmCIF format, chain NB [auth K] mmCIF format, chain S [auth B] mmCIF format, chain SB [auth L] mmCIF format, chain VA [auth G] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	EA [auth D] FA [auth D] IB [auth J] LA [auth E] MB [auth K] EA [auth D], FA [auth D], IB [auth J], LA [auth E], MB [auth K], NB [auth K], S [auth B], SB [auth L], VA [auth G], X [auth C], Y [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain IB [auth J] Focus chain LA [auth E] Focus chain MB [auth K] Focus chain NB [auth K] Focus chain S [auth B] Focus chain SB [auth L] Focus chain VA [auth G] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain IB [auth J] Focus chain LA [auth E] Focus chain MB [auth K] Focus chain NB [auth K] Focus chain S [auth B] Focus chain SB [auth L] Focus chain VA [auth G] Focus chain X [auth C] Focus chain Y [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain CB [auth I] SDF format, chain DA [auth D] SDF format, chain DB [auth I] SDF format, chain HB [auth J] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain O [auth A] SDF format, chain QA [auth F] SDF format, chain RB [auth L] SDF format, chain UA [auth G] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth I] MOL2 format, chain HB [auth J] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain RB [auth L] MOL2 format, chain UA [auth G] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth I] mmCIF format, chain HB [auth J] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain RB [auth L] mmCIF format, chain UA [auth G] mmCIF format, chain W [auth C]	CA [auth D] CB [auth I] DA [auth D] DB [auth I] HB [auth J] CA [auth D], CB [auth I], DA [auth D], DB [auth I], HB [auth J], JA [auth E], KA [auth E], O [auth A], QA [auth F], RB [auth L], UA [auth G], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain HB [auth J] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain O [auth A] Focus chain QA [auth F] Focus chain RB [auth L] Focus chain UA [auth G] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain HB [auth J] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain O [auth A] Focus chain QA [auth F] Focus chain RB [auth L] Focus chain UA [auth G] Focus chain W [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EB [auth I] SDF format, chain GA [auth D] SDF format, chain JB [auth J] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OB [auth K] SDF format, chain P [auth A] SDF format, chain RA [auth F] SDF format, chain T [auth B] SDF format, chain TB [auth L] SDF format, chain WA [auth G] SDF format, chain Z [auth C] SDF format, chain ZA [auth H] MOL2 format, chain EB [auth I] MOL2 format, chain GA [auth D] MOL2 format, chain JB [auth J] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OB [auth K] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TB [auth L] MOL2 format, chain WA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth H] mmCIF format, chain EB [auth I] mmCIF format, chain GA [auth D] mmCIF format, chain JB [auth J] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain OB [auth K] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TB [auth L] mmCIF format, chain WA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth H]	EB [auth I] GA [auth D] JB [auth J] MA [auth E] NA [auth E] EB [auth I], GA [auth D], JB [auth J], MA [auth E], NA [auth E], OB [auth K], P [auth A], RA [auth F], T [auth B], TB [auth L], WA [auth G], Z [auth C], ZA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EB [auth I] Focus chain GA [auth D] Focus chain JB [auth J] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OB [auth K] Focus chain P [auth A] Focus chain RA [auth F] Focus chain T [auth B] Focus chain TB [auth L] Focus chain WA [auth G] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain EB [auth I] Focus chain GA [auth D] Focus chain JB [auth J] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OB [auth K] Focus chain P [auth A] Focus chain RA [auth F] Focus chain T [auth B] Focus chain TB [auth L] Focus chain WA [auth G] Focus chain Z [auth C] Focus chain ZA [auth H]

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, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.193 (Depositor), 0.197 (DCC)
R-Value Work: 0.151 (Depositor), 0.158 (DCC)
R-Value Observed: 0.153 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.906	α = 90
b = 156.79	β = 95.29
c = 170.161	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary