4EH1 | pdb_00004eh1

Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase from Vibrio cholerae O1 biovar El Tor

PDB DOI: https://doi.org/10.2210/pdb4EH1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-04-02 Released: 2012-04-25
Deposition Author(s): Kim, Y., Gu, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.219 (Depositor), 0.215 (DCC)
R-Value Work:
0.165 (Depositor), 0.164 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase from Vibrio cholerae O1 biovar El Tor

Kim, Y., Gu, M., Hasseman, J., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 56.38 kDa
Atom Count: 4,284
Modeled Residue Count: 474
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavohemoprotein	A, B	243	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: hmp, VC_A0183 EC: 1.14.12.17
UniProt
Find proteins for Q9KMY3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMY3 Go to UniProtKB: Q9KMY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KMY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	H [auth A], J [auth A], K [auth B], M [auth B], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	D [auth A], G [auth A], I [auth A], O [auth B], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.219 (Depositor), 0.215 (DCC)
R-Value Work: 0.165 (Depositor), 0.164 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.329	α = 90
b = 93.329	β = 90
c = 112.594	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing