3IPJ | pdb_00003ipj

The crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile

PDB DOI: https://doi.org/10.2210/pdb3IPJ/pdb

Classification: TRANSFERASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-08-17 Released: 2009-10-20
Deposition Author(s): Zhang, R., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.170 (Depositor), 0.170 (DCC)
R-Value Work:
0.133 (Depositor), 0.138 (DCC)
R-Value Observed:
0.135 (Depositor)

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

Literature

The crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile

Zhang, R., Bigelow, L., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 21.7 kDa
Atom Count: 1,767
Modeled Residue Count: 190
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system, IIabc component	A, B	95	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD0469, GI:115249482 EC: 2.7.1.69
UniProt
Find proteins for Q188R0 (Clostridioides difficile (strain 630)) Explore Q188R0 Go to UniProtKB: Q188R0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q188R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.170 (Depositor), 0.170 (DCC)
R-Value Work: 0.133 (Depositor), 0.138 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.635	α = 90
b = 34.734	β = 90.07
c = 72.195	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.