1RB9 | pdb_00001rb9

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS REFINED ANISOTROPICALLY AT 0.92 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1RB9/pdb

• Classification: IRON-SULFUR PROTEIN
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-21 Released: 1999-02-16 
• Deposition Author(s): Dauter, Z., Butterworth, S., Sieker, L.C., Sheldrick, G., Wilson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Work: 
  0.080 (DCC) 

Starting Model: experimental

Literature

Anisotropic Refinement of Rubredoxin from Desulfovibrio Vulgaris

Dauter, Z., Butterworth, S., Sieker, L.C., Sheldrick, G., Wilson, K.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.76 kDa 
• Atom Count: 558 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUBREDOXIN	A	52	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0
UniProt
Find proteins for P00269 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P00269  Go to UniProtKB:  P00269

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Work:  0.080 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 19.97	α = 90
b = 41.45	β = 108.3
c = 24.41	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	model building
SHELXL-97	refinement
MOSFLM	data reduction
Agrovata	data scaling
SHELXL-97	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Dauter, Z., Butterworth, S., Sieker, L.C., Sheldrick, G., Wilson, K.S.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary