3V7B | pdb_00003v7b

Dip2269 protein from corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb3V7B/pdb
Entry: 3V7B supersedes: 2I8G

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-20 Released: 2012-01-11
Deposition Author(s): Osipiuk, J., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.228 (Depositor), 0.242 (DCC)
R-Value Work:
0.177 (Depositor), 0.192 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3V7B

This is version 1.2 of the entry. See complete history.

Literature

Dip2269 protein from corynebacterium diphtheriae.

Osipiuk, J., Duggan, E., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 33.65 kDa
Atom Count: 2,528
Modeled Residue Count: 289
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	151	Corynebacterium diphtheriae	Mutation(s): 0 Gene Names: DIP2269
UniProt
Find proteins for Q6NEK4 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEK4 Go to UniProtKB: Q6NEK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NEK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.228 (Depositor), 0.242 (DCC)
R-Value Work: 0.177 (Depositor), 0.192 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.002	α = 90
b = 66.752	β = 90
c = 70.287	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 2I8G

Revision History (Full details and data files)

Version 1.0: 2012-01-11
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.