2WFB | pdb_00002wfb

High resolution structure of the apo form of the orange protein (ORP) from Desulfovibrio gigas

• PDB DOI: https://doi.org/10.2210/pdb2WFB/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Megalodesulfovibrio gigas
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-04-03 Released: 2010-05-26 
• Deposition Author(s): Najmudin, S., Bonifacio, C., Duarte, A.G., Pereira, A.S., Moura, I., Moura, J.M., Romao, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

High Resolution Crystal Structure of the Apo Form of the Orange Protein (Apo-Orp) from Desulfovibrio Gigas

Najmudin, S., Bonifacio, C., Duarte, A.G., Moura, I., Moura, J.G., Romao, M.J.

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: 12.46 kDa 
• Atom Count: 958 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE UNCHARACTERIZED PROTEIN ORP	A	120	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for Q5DUA6 (Megalodesulfovibrio gigas) Explore Q5DUA6  Go to UniProtKB:  Q5DUA6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.078	α = 90
b = 43.078	β = 90
c = 106.085	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Najmudin, S., Bonifacio, C., Duarte, A.G., Pereira, A.S., Moura, I., Moura, J.M., Romao, M.J.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description