6D0G | pdb_00006d0g

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

PDB DOI: https://doi.org/10.2210/pdb6D0G/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: 1.78 Å
R-Value Free:
0.210 (Depositor), 0.218 (DCC)
R-Value Work:
0.174 (Depositor), 0.183 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

1.78 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: 36.37 kDa
Atom Count: 2,689
Modeled Residue Count: 299
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin family protein	A	318	Acinetobacter baumannii	Mutation(s): 0 Gene Names: yhhW_2, yhhW_1, A388_00159, A7A65_05705, A7M90_08420, A7N09_08935, AZE33_00735, B4R90_09220, B9X91_00175, BGC29_04645... yhhW_2, yhhW_1, A388_00159, A7A65_05705, A7M90_08420, A7N09_08935, AZE33_00735, B4R90_09220, B9X91_00175, BGC29_04645, CAS83_08120, CBE85_14535, CEJ63_12860, CHQ89_16690, CPI82_15400, CV954_18565, LV38_01393 EC: 1.13.11.24

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.210 (Depositor), 0.218 (DCC)
R-Value Work: 0.174 (Depositor), 0.183 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.883	α = 90
b = 73.616	β = 90
c = 202.741	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

View more in-depth experimental data

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: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary