3IVP | pdb_00003ivp

The structure of a possible transposon-related DNA-binding protein from Clostridium difficile 630.

PDB DOI: https://doi.org/10.2210/pdb3IVP/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-01 Released: 2009-09-22
Deposition Author(s): Tan, K., Marshall, N., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.235 (Depositor), 0.314 (DCC)
R-Value Work:
0.200 (Depositor), 0.293 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3IVP

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

Literature

The structure of a possible transposon-related DNA-binding protein from Clostridium difficile 630.

Tan, K., Marshall, N., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 58.82 kDa
Atom Count: 3,805
Modeled Residue Count: 452
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transposon-related DNA-binding protein	A, B, C, D	126	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD3330, Clostridium difficile
UniProt
Find proteins for Q180H4 (Clostridioides difficile (strain 630)) Explore Q180H4 Go to UniProtKB: Q180H4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q180H4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain G [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain G [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	E [auth C], F [auth C], G [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [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: 2.02 Å
R-Value Free: 0.235 (Depositor), 0.314 (DCC)
R-Value Work: 0.200 (Depositor), 0.293 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.326	α = 90
b = 69.829	β = 90
c = 170.359	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Jedrzejczak, R.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2024-10-16
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.