3PG5 | pdb_00003pg5

Crystal structure of protein DIP2308 from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR78

PDB DOI: https://doi.org/10.2210/pdb3PG5/pdb

Classification: Structural genomics, Unknown function
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-30 Released: 2010-12-22
Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Lee, D., Ciccosanti, C., Sahdev, S., Nair, R., Rost, B., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.235 (Depositor), 0.251 (DCC)
R-Value Work:
0.187 (Depositor), 0.204 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of protein DIP2308 from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR78

Forouhar, F., Lew, S., Seetharaman, J., Lee, D., Ciccosanti, C., Sahdev, S., Nair, R., Rost, B., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 164.25 kDa
Atom Count: 9,613
Modeled Residue Count: 1,213
Deposited Residue Count: 1,444
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	361	Corynebacterium diphtheriae	Mutation(s): 0 Gene Names: DIP2308
UniProt
Find proteins for Q6NEG6 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEG6 Go to UniProtKB: Q6NEG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NEG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 3.30 Å
R-Value Free: 0.235 (Depositor), 0.251 (DCC)
R-Value Work: 0.187 (Depositor), 0.204 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.963	α = 90
b = 199.963	β = 90
c = 106.58	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELX	model building
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-22

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-02-22
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary