4M87 | pdb_00004m87

Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) from Neisseria meningitidis in complex with NAD+

PDB DOI: https://doi.org/10.2210/pdb4M87/pdb

Classification: OXIDOREDUCTASE
Organism(s): Neisseria meningitidis FAM18
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-13 Released: 2013-10-02
Deposition Author(s): Nanson, J.D., Forwood, J.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.189 (Depositor), 0.197 (DCC)
R-Value Work:
0.169 (Depositor), 0.177 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4M87

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) from Neisseria meningitidis in complex with NAD+

Nanson, J.D., Forwood, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 56.77 kDa
Atom Count: 4,100
Modeled Residue Count: 503
Deposited Residue Count: 522
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B	261	Neisseria meningitidis FAM18	Mutation(s): 0 Gene Names: fabI, NMC1834 EC: 1.3.1.9
UniProt
Find proteins for A1KVU8 (Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18)) Explore A1KVU8 Go to UniProtKB: A1KVU8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1KVU8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-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: 2.25 Å
R-Value Free: 0.189 (Depositor), 0.197 (DCC)
R-Value Work: 0.169 (Depositor), 0.177 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.1	α = 90
b = 91.1	β = 90
c = 240.84	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-02
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.