3LOR

The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to 2.2A

PDB DOI: https://doi.org/10.2210/pdb3LOR/pdb

Classification: ISOMERASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-04 Released: 2010-03-16
Deposition Author(s): Stein, A.J., Osipiuk, J., Weger, A., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.259 (Depositor), 0.276 (DCC)
R-Value Work:
0.212 (Depositor), 0.228 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to 2.2A

Stein, A.J., Osipiuk, J., Weger, A., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 73.38 kDa
Atom Count: 4,860
Modelled Residue Count: 610
Deposited Residue Count: 640
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol-disulfide isomerase and thioredoxins	A, B, C, D	160	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: cg1043, Cgl0914
UniProt
Find proteins for Q8NRX7 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NRX7 Go to UniProtKB: Q8NRX7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NRX7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D]	E [auth A], F [auth B], I [auth C], J [auth D], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.259 (Depositor), 0.276 (DCC)
R-Value Work: 0.212 (Depositor), 0.228 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.19	α = 90
b = 78.892	β = 90
c = 124.229	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary