6OK3 | pdb_00006ok3

Crystal structure of Sel1 repeat protein from Oxalobacter formigenes

PDB DOI: https://doi.org/10.2210/pdb6OK3/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.247 (Depositor), 0.253 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6OK3

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 120.14 kDa
Atom Count: 8,528
Modeled Residue Count: 1,015
Deposited Residue Count: 1,046
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sel1 repeat protein	A	523	Oxalobacter formigenes OXCC13	Mutation(s): 0 Gene Names: OFBG_00935 EC: 3.5.2.6
UniProt
Find proteins for C3X9N1 (Oxalobacter formigenes OXCC13) Explore C3X9N1 Go to UniProtKB: C3X9N1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3X9N1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sel1 repeat protein	B	523	Oxalobacter formigenes OXCC13	Mutation(s): 0 Gene Names: OFBG_00935 EC: 3.5.2.6
UniProt
Find proteins for C3X9N1 (Oxalobacter formigenes OXCC13) Explore C3X9N1 Go to UniProtKB: C3X9N1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3X9N1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.247 (Depositor), 0.253 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.059	α = 90
b = 44.976	β = 92.84
c = 142.734	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.