5IJG | pdb_00005ijg

Crystal structure of O-acetylhomoserine sulfhydrolase from Brucella melitensis at 2.0 A resolution

PDB DOI: https://doi.org/10.2210/pdb5IJG/pdb

Classification: HYDROLASE
Organism(s): Brucella melitensis bv. 1 str. 16M
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-02 Released: 2017-04-05
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Koolikova, V.V., Kotlov, M.I., Demidkina, T.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.223 (Depositor), 0.227 (DCC)
R-Value Work:
0.170 (Depositor), 0.177 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of O-acetylhomoserine sulfhydrolase from Brucella melitensis at 2.0 A resolution

Boyko, K.M., Nikolaeva, A.Y., Koolikova, V., Demidkina, T.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 92.19 kDa
Atom Count: 6,131
Modeled Residue Count: 756
Deposited Residue Count: 854
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cys/Met metabolism pyridoxal-phosphate-dependent enzyme	A, B	427	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0 Gene Names: BMEI0103, BAWG_0092 EC: 2.5.1.48
UniProt
Find proteins for Q8YJI0 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YJI0 Go to UniProtKB: Q8YJI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YJI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223 (Depositor), 0.227 (DCC)
R-Value Work: 0.170 (Depositor), 0.177 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.71	α = 90
b = 109.71	β = 90
c = 110.77	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Nikolaeva, A.Y.

Koolikova, V.V.

Demidkina, T.V.

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.