3K1Y

X-ray structure of oxidoreductase from corynebacterium diphtheriae. orthorombic crystal form, northeast structural genomics consortium target cdr100d

PDB DOI: https://doi.org/10.2210/pdb3K1Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-29 Released: 2009-10-20
Deposition Author(s): Kuzin, A., Lew, S., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor), 0.230 (DCC)
R-Value Work:
0.229 (Depositor), 0.220 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target CdR100D

Kuzin, A., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 124.28 kDa
Atom Count: 8,235
Modelled Residue Count: 1,085
Deposited Residue Count: 1,146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
oxidoreductase	A, B, C, D, E A, B, C, D, E, F	191	Corynebacterium diphtheriae	Mutation(s): 0 Gene Names: DIP1437
UniProt
Find proteins for Q6NGS1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGS1 Go to UniProtKB: Q6NGS1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NGS1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain S [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain S [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain S [auth E]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth E], U [auth F], V [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.241 (Depositor), 0.230 (DCC)
R-Value Work: 0.229 (Depositor), 0.220 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.17	α = 90
b = 141.379	β = 90
c = 201.565	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALA	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary