4YWN | pdb_00004ywn

Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

PDB DOI: https://doi.org/10.2210/pdb4YWN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium avium 104
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-20 Released: 2015-04-01
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:
0.215 (Depositor), 0.218 (DCC)
R-Value Work:
0.179 (Depositor), 0.182 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

Abendroth, J., Jensen, M., Arakaki, T.L., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 35.04 kDa
Atom Count: 2,207
Modeled Residue Count: 279
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-fmn oxidoreductase	A, B	165	Mycobacterium avium 104	Mutation(s): 0 Gene Names: MAV_4912
UniProt
Find proteins for A0A0J9X290 (Mycobacterium avium (strain 104)) Explore A0A0J9X290 Go to UniProtKB: A0A0J9X290
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0J9X290
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.215 (Depositor), 0.218 (DCC)
R-Value Work: 0.179 (Depositor), 0.182 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.26	α = 90
b = 50.26	β = 90
c = 229.59	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-04-01

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-04-01
Type: Initial release
Version 1.1: 2015-08-26
Changes: Experimental preparation
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.3: 2023-09-27
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.