1E9V | pdb_00001e9v

XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS

• PDB DOI: https://doi.org/10.2210/pdb1E9V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Nitratidesulfovibrio vulgaris
• Mutation(s): No 


• Deposited: 2000-10-27 Released: 2001-10-25 
• Deposition Author(s): Cooper, S.J., Bailey, S., Rizkallah, P.J., Lindley, P.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.197 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.151 (DCC) 

Literature

Ferricyanide Soaked Hybrid Cluster Protein at 1.2A and Xenon Mapping of the Hydrophobic Cavity at 1.8A

Cooper, S.J., Garner, C.D., Hagen, W.R., Lindley, P.F., Bailey, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.84 kDa 
• Atom Count: 5,026 
• Modeled Residue Count: 553 
• Deposited Residue Count: 553 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYLAMINE REDUCTASE	A	553	Nitratidesulfovibrio vulgaris	Mutation(s): 0  EC: 1.7 (PDB Primary Data), 1.7.99.1 (UniProt)
UniProt
Find proteins for P31101 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P31101  Go to UniProtKB:  P31101

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSO	B [auth A]	IRON/SULFUR/OXYGEN HYBRID CLUSTER Fe4 O3 S3 JQPFOUXUGPAEOB-UHFFFAOYSA-N
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
XE	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
TRS	T [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	S [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	Q [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	R [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.197 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.151 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.62	α = 90
b = 64.598	β = 90
c = 152.254	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-25 
Deposition Author(s): Cooper, S.J., Bailey, S., Rizkallah, P.J., Lindley, P.F.

Revision History  

• Version 1.0: 2001-10-25
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2013-03-27
  Changes: Database references, Non-polymer description, Other, Source and taxonomy, Structure summary
• Version 2.0: 2020-12-23
  Changes: Advisory, Atomic model, Derived calculations, Other
• Version 2.1: 2024-11-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary