3CP3 | pdb_00003cp3

Crystal structure of conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb3CP3/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-03-31 Released: 2008-04-15
Deposition Author(s): Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.229 (Depositor), 0.221 (DCC)
R-Value Work:
0.188 (Depositor), 0.185 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae.

Kim, Y., Wu, R., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.91 kDa
Atom Count: 1,191
Modeled Residue Count: 127
Deposited Residue Count: 148
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	148	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0 Gene Names: DIP1874
UniProt
Find proteins for Q6NFL3 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NFL3 Go to UniProtKB: Q6NFL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NFL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229 (Depositor), 0.221 (DCC)
R-Value Work: 0.188 (Depositor), 0.185 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.374	α = 90
b = 59.374	β = 90
c = 98.948	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-04-03
Changes: Refinement description

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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.