8CXA | pdb_00008cxa

Crystal Structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium smegmatis with bound NAD

PDB DOI: https://doi.org/10.2210/pdb8CXA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-20 Released: 2022-07-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.182 (Depositor), 0.182 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (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-oxoacyl-[acyl-carrier-protein] reductase with bound NAD

Bolejack, M.J., deBouver, N.D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 118.4 kDa
Atom Count: 8,364
Modeled Residue Count: 997
Deposited Residue Count: 1,092
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] reductase	A, B, C, D	273	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: KPHS_35560 EC: 1.1.1.100
UniProt
Find proteins for A0QVD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QVD5 Go to UniProtKB: A0QVD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QVD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.182 (Depositor), 0.182 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.86	α = 90
b = 128.78	β = 96.03
c = 60.9	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.