4R88

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-fluorocytosine

PDB DOI: https://doi.org/10.2210/pdb4R88/pdb
Entry: 4R88 supersedes: 4JNR

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae 30660/NJST258_1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-29 Released: 2014-09-17
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Hitchcock, D.S., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.201
R-Value Work: 0.165
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-fluorocytosine

Fedorov, A.A., Fedorov, E.V., Hitchcock, D.S., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 293.1 kDa
Atom Count: 20,876
Modelled Residue Count: 2,469
Deposited Residue Count: 2,586
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B, C, D, E A, B, C, D, E, F	431	Klebsiella pneumoniae 30660/NJST258_1	Mutation(s): 0 Gene Names: KPNJ1_03949 EC: 3.5.4.1
UniProt
Find proteins for A0A0E1CHI1 (Klebsiella pneumoniae 30660/NJST258_1) Explore A0A0E1CHI1 Go to UniProtKB: A0A0E1CHI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0E1CHI1
Sequence Annotations Expand
Reference Sequence

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 DB [auth E] MOL2 format, chain DB [auth E]	DB [auth E]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain DB [auth E] Interactions & Density Focus chain DB [auth E]
1LD Query on 1LD Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain GB [auth F] SDF format, chain LA [auth D] SDF format, chain S [auth B] SDF format, chain UA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth E]	DA [auth C] G [auth A] GB [auth F] LA [auth D] S [auth B] DA [auth C], G [auth A], GB [auth F], LA [auth D], S [auth B], UA [auth E]	5-fluorocytosine C₄ H₄ F N₃ O XRECTZIEBJDKEO-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain G [auth A] Focus chain GB [auth F] Focus chain LA [auth D] Focus chain S [auth B] Focus chain UA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain G [auth A] Focus chain GB [auth F] Focus chain LA [auth D] Focus chain S [auth B] Focus chain UA [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain LB [auth F] SDF format, chain W [auth B] MOL2 format, chain LB [auth F] MOL2 format, chain W [auth B]	LB [auth F], W [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain LB [auth F] Focus chain W [auth B] Interactions & Density Focus chain LB [auth F] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IB [auth F] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain U [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E]	FA [auth C] FB [auth F] GA [auth C] HA [auth C] I [auth A] FA [auth C], FB [auth F], GA [auth C], HA [auth C], I [auth A], IB [auth F], J [auth A], M [auth A], N [auth A], NA [auth D], OA [auth D], PA [auth D], U [auth B], WA [auth E], X [auth B], XA [auth E], YA [auth E], ZA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IB [auth F] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IB [auth F] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EB [auth E] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] EB [auth E] JA [auth C] AA [auth B], BA [auth B], CA [auth B], EB [auth E], JA [auth C], KA [auth C], O [auth A], P [auth A], Q [auth A], R [auth A], RA [auth D], SA [auth D], TA [auth D], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain IA [auth C] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain QA [auth D] SDF format, chain V [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain V [auth B]	AB [auth E] BB [auth E] CB [auth E] IA [auth C] JB [auth F] AB [auth E], BB [auth E], CB [auth E], IA [auth C], JB [auth F], K [auth A], KB [auth F], L [auth A], QA [auth D], V [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain IA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain QA [auth D] Focus chain V [auth B] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain IA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain QA [auth D] Focus chain V [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain H [auth A] SDF format, chain HB [auth F] SDF format, chain MA [auth D] SDF format, chain T [auth B] SDF format, chain VA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain MA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth E]	EA [auth C] H [auth A] HB [auth F] MA [auth D] T [auth B] EA [auth C], H [auth A], HB [auth F], MA [auth D], T [auth B], VA [auth E]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain H [auth A] Focus chain HB [auth F] Focus chain MA [auth D] Focus chain T [auth B] Focus chain VA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain H [auth A] Focus chain HB [auth F] Focus chain MA [auth D] Focus chain T [auth B] Focus chain VA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.201
R-Value Work: 0.165
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.954	α = 90
b = 162.419	β = 90
c = 184.047	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

This entry supersedes: 4JNR

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description