6D0P

1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6D0P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-10 Released: 2018-04-25
Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Dubrovska, I., Kiryukhina, O., Endres, M., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.190
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii

Minasov, G., Shuvalova, L., Brunzelle, J.S., Dubrovska, I., Kiryukhina, O., Endres, M., Anderson, W.F., Satchell, K.J.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 131.66 kDa
Atom Count: 10,771
Modelled Residue Count: 1,152
Deposited Residue Count: 1,172
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin family protein	A, B, C, D	293	Acinetobacter baumannii	Mutation(s): 0 Gene Names: A7N09_17085, B4R90_18685, B9X95_09530, BGC29_11425, BWP00_02730, CPI82_04080, CV950_06630, CV954_00950, IX87_13390 EC: 1.13.11.24
UniProt
Find proteins for A0A0C0C2K2 (Acinetobacter baumannii) Explore A0A0C0C2K2 Go to UniProtKB: A0A0C0C2K2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0C0C2K2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain V [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth D]	J [auth A], O [auth B], V [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain V [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain V [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C]	H [auth A], I [auth A], M [auth B], Q [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D]	R [auth C], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain R [auth C] Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	G [auth A], L [auth B], P [auth C], T [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D]	K [auth B], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain S [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.190
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m36d0p

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.481	α = 90
b = 131.977	β = 103.58
c = 123.987	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-04-25

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-04-25
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary