4R7W | pdb_00004r7w

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

PDB DOI: https://doi.org/10.2210/pdb4R7W/pdb
Entry: 4R7W supersedes: 4JNS

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

Deposited: 2014-08-28 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: 1.90 Å
R-Value Free:
0.242 (Depositor), 0.236 (DCC)
R-Value Work:
0.198 (Depositor), 0.193 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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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 phosphonocytosine

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

To be published.

Macromolecule Content

Total Structure Weight: 290.62 kDa
Atom Count: 20,980
Modeled Residue Count: 2,467
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O7U Query on O7U Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain DA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth F]	DA [auth F] H [auth A] M [auth B] P [auth C] V [auth D] DA [auth F], H [auth A], M [auth B], P [auth C], V [auth D], Z [auth E]	(2R)-2-amino-2,5-dihydro-1,5,2-diazaphosphinin-6(1H)-one 2-oxide C₃ H₆ N₃ O₂ P GGLLBAYBJJLFCT-SECBINFHSA-N		Interactions Focus chain DA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain V [auth D] Focus chain Z [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain I [auth A] SDF format, chain BA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth E]	BA [auth E], I [auth A], R [auth C], S [auth C], W [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain I [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain I [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth E]	AA [auth E] J [auth A] K [auth A] N [auth B] T [auth C] AA [auth E], J [auth A], K [auth A], N [auth B], T [auth C], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain U [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain CA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain CA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain CA [auth F]	CA [auth F] G [auth A] L [auth B] O [auth C] U [auth D] CA [auth F], G [auth A], L [auth B], O [auth C], U [auth D], Y [auth E]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.242 (Depositor), 0.236 (DCC)
R-Value Work: 0.198 (Depositor), 0.193 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.167	α = 90
b = 147.808	β = 90
c = 185.336	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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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

This entry supersedes: 4JNS

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