3M6J | pdb_00003m6j

Crystal structure of unknown function protein from Leptospirillum rubarum

• PDB DOI: https://doi.org/10.2210/pdb3M6J/pdb

• Classification: structural genomics, unknown function
• Organism(s): Leptospirillum rubarum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-15 Released: 2010-03-31 
• Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of unknown function protein from Leptospirillum rubarum

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

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.63 kDa 
• Atom Count: 4,785 
• Modeled Residue Count: 526 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B, C, D	145	Leptospirillum rubarum	Mutation(s): 0  Gene Names: UBAL2_80490123
UniProt
Find proteins for A0A059XY95 (Leptospirillum ferriphilum YSK) Explore A0A059XY95  Go to UniProtKB:  A0A059XY95

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.843	α = 90
b = 58.275	β = 100.99
c = 93.279	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2021-12-01
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2024-10-09
  Changes: Data collection, Structure summary