6OK0 | pdb_00006ok0

Crystal structure of Sel1 repeat protein from Oxalobacter formigenes

• PDB DOI: https://doi.org/10.2210/pdb6OK0/pdb

• Classification: HYDROLASE
• Organism(s): Oxalobacter formigenes OXCC13
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-12 Released: 2020-04-15 
• Deposition Author(s): Chang, C., Tesar, C., Endres, M., Babnigg, G., Hassan, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of Sel1 repeat protein from Oxalobacter formigenes

Chang, C., Tesar, C., Endres, M., Babnigg, G., Hassan, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.27 kDa 
• Atom Count: 4,231 
• Modeled Residue Count: 525 
• Deposited Residue Count: 604 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sel1 repeat protein	A	151	Oxalobacter formigenes OXCC13	Mutation(s): 0  Gene Names: OFBG_00636 EC: 3.5.2.6
UniProt
Find proteins for C3X8T2 (Oxalobacter formigenes OXCC13) Explore C3X8T2  Go to UniProtKB:  C3X8T2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sel1 repeat protein	B	151	Oxalobacter formigenes OXCC13	Mutation(s): 0  Gene Names: OFBG_00636 EC: 3.5.2.6
UniProt
Find proteins for C3X8T2 (Oxalobacter formigenes OXCC13) Explore C3X8T2  Go to UniProtKB:  C3X8T2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sel1 repeat protein	C	151	Oxalobacter formigenes OXCC13	Mutation(s): 0  Gene Names: OFBG_00636 EC: 3.5.2.6
UniProt
Find proteins for C3X8T2 (Oxalobacter formigenes OXCC13) Explore C3X8T2  Go to UniProtKB:  C3X8T2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sel1 repeat protein	D	151	Oxalobacter formigenes OXCC13	Mutation(s): 0  Gene Names: OFBG_00636 EC: 3.5.2.6
UniProt
Find proteins for C3X8T2 (Oxalobacter formigenes OXCC13) Explore C3X8T2  Go to UniProtKB:  C3X8T2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
IMD	G [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	F [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36ok0

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.768	α = 68.54
b = 68.587	β = 79.25
c = 74.365	γ = 89.97

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Chang, C., Tesar, C., Endres, M., Babnigg, G., Hassan, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2025-04-02
  Changes: Data collection, Database references, Structure summary