4R88 | pdb_00004r88

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B, C, D, E, F	431	Klebsiella pneumoniae 30660/NJST258_1	Mutation(s): 0  Gene Names: KPNJ1_03949 EC: 3.5.4.1

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	DB [auth E]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
1LD	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
PEG	LB [auth F], W [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	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
EDO	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
ACY	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
FE2	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Hitchcock, D.S., Raushel, F.M., Almo, S.C.
• This entry supersedes: 4JNR

Revision History  

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