4GI5 | pdb_00004gi5

Crystal Structure Of a Putative quinone reductase from Klebsiella pneumoniae (Target PSI-013613)

PDB DOI: https://doi.org/10.2210/pdb4GI5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-08 Released: 2012-08-22
Deposition Author(s): Kumar, P.R., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Gizzi, A., Glen, S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Washington, E., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.163 (Depositor), 0.165 (DCC)
R-Value Work:
0.144 (Depositor)
R-Value Observed:
0.145 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a quinone reductase from Klebsiella pneumoniae with bound FAD

Kumar, P.R., Hillerich, B., Love, J., Seidel, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 66.09 kDa
Atom Count: 4,787
Modeled Residue Count: 520
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
quinone reductase	A, B	280	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: KPN78578_46790, KPN_04757
UniProt
Find proteins for A6THR9 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6THR9 Go to UniProtKB: A6THR9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6THR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], K [auth B], L [auth B], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	D [auth A], I [auth B]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.163 (Depositor), 0.165 (DCC)
R-Value Work: 0.144 (Depositor)
R-Value Observed: 0.145 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.834	α = 90
b = 106.573	β = 90
c = 109.326	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-08-22
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary