6B9U | pdb_00006b9u

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Brucella melitensis complexed with NADH

PDB DOI: https://doi.org/10.2210/pdb6B9U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-11 Released: 2017-10-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.160 (Depositor), 0.163 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Brucella melitensis complexed with NADH

Pierce, P.G., Phan, J.N., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 54.97 kDa
Atom Count: 3,887
Modeled Residue Count: 486
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase	A, B	257	Brucella abortus 2308	Mutation(s): 0 Gene Names: BAB2_0975
UniProt
Find proteins for Q2YJS1 (Brucella abortus (strain 2308)) Explore Q2YJS1 Go to UniProtKB: Q2YJS1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YJS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.160 (Depositor), 0.163 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.13	α = 90
b = 88.13	β = 90
c = 111.95	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2023-10-04
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.