4IQG

Crystal structure of BPRO0239 oxidoreductase from Polaromonas sp. JS666 in NADP bound form

PDB DOI: https://doi.org/10.2210/pdb4IQG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Polaromonas sp. JS666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-11 Released: 2013-01-30
Deposition Author(s): Niedzialkowska, E., Majorek, K.A., Porebski, P.J., Al Obaidi, N., Hammonds, J., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.173
R-Value Work: 0.148
R-Value Observed: 0.150

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 oxidoreductase from Polaromonas sp. in NADP bound form

Niedzialkowska, E., Majorek, K.A., Porebski, P.J., Al Obaidi, N., Hammonds, J., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 118.5 kDa
Atom Count: 7,931
Modelled Residue Count: 977
Deposited Residue Count: 1,084
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A [auth C], B [auth A], C [auth B], D	271	Polaromonas sp. JS666	Mutation(s): 0 Gene Names: Bpro_0239
UniProt
Find proteins for Q12GY8 (Polaromonas sp. (strain JS666 / ATCC BAA-500)) Explore Q12GY8 Go to UniProtKB: Q12GY8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12GY8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain P [auth D] MOL2 format, chain H [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth D] mmCIF format, chain H [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth D]	H [auth C], L [auth A], M [auth B], P [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain H [auth C] Focus chain L [auth A] Focus chain M [auth B] Focus chain P [auth D] Interactions & Density Focus chain H [auth C] Focus chain L [auth A] Focus chain M [auth B] Focus chain P [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain E [auth C] SDF format, chain N [auth B] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain E [auth C] MOL2 format, chain N [auth B] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain E [auth C] mmCIF format, chain N [auth B]	E [auth C] F [auth C] G [auth C] I [auth A] J [auth A] E [auth C], F [auth C], G [auth C], I [auth A], J [auth A], N [auth B], O [auth B], R [auth D], S [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth D] Focus chain S [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.173
R-Value Work: 0.148
R-Value Observed: 0.150
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M3NK5K

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.142	α = 90
b = 97.71	β = 97.32
c = 70.665	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-30

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary