4R85 | pdb_00004r85

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

PDB DOI: https://doi.org/10.2210/pdb4R85/pdb
Entry: 4R85 supersedes: 4JNP

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: 1.80 Å
R-Value Free:
0.187 (Depositor), 0.188 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

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-methylcytosine

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

To be published.

Macromolecule Content

Total Structure Weight: 291.15 kDa
Atom Count: 21,294
Modeled Residue Count: 2,469
Deposited Residue Count: 2,586
Unique protein chains: 1

Macromolecules

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| 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
17E Query on 17E Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain GA [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain GA [auth F] mmCIF format, chain AA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain GA [auth F]	AA [auth E] G [auth A] GA [auth F] L [auth B] R [auth C] AA [auth E], G [auth A], GA [auth F], L [auth B], R [auth C], W [auth D]	5-methylcytosine C₅ H₇ N₃ O LRSASMSXMSNRBT-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain K [auth A] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain K [auth A]	CA [auth E] DA [auth E] EA [auth E] FA [auth F] I [auth A] CA [auth E], DA [auth E], EA [auth E], FA [auth F], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain HA [auth F] SDF format, chain BA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain HA [auth F] MOL2 format, chain BA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain HA [auth F] mmCIF format, chain BA [auth E]	BA [auth E] H [auth A] HA [auth F] M [auth B] S [auth C] BA [auth E], H [auth A], HA [auth F], M [auth B], S [auth C], X [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.187 (Depositor), 0.188 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.481	α = 90
b = 137.669	β = 118.03
c = 112.093	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

This entry supersedes: 4JNP

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