3JZV | pdb_00003jzv

Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.

• PDB DOI: https://doi.org/10.2210/pdb3JZV/pdb

• Classification: structural genomics, unknown function
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-24 Released: 2009-10-13 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.65 kDa 
• Atom Count: 1,156 
• Modeled Residue Count: 148 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein Rru_A2000	A	166	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: Rru_A2000 EC: 2.8.4.6
UniProt
Find proteins for Q2RSU5 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RSU5  Go to UniProtKB:  Q2RSU5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.886	α = 90
b = 90.886	β = 90
c = 161.252	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary