3OMD | pdb_00003omd

Crystal structure of unknown function protein from Leptospirillum rubarum

• PDB DOI: https://doi.org/10.2210/pdb3OMD/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Leptospirillum rubarum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-26 Released: 2010-09-15 
• Deposition Author(s): Chang, C., Xu, X., Cui, H., Chen, Z., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal structure of unknown function protein from Leptospirillum rubarum

Chang, C., Xu, X., Cui, H., Chen, Z., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,894 
• Modeled Residue Count: 290 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	145	Leptospirillum rubarum	Mutation(s): 0  Gene Names: UBAL2_82410030

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
OCS	A, B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.91	α = 90
b = 66.259	β = 90
c = 78.044	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Chang, C., Xu, X., Cui, H., Chen, Z., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary