3LV9 | pdb_00003lv9

Crystal structure of CBS domain of a putative transporter from Clostridium difficile 630

PDB DOI: https://doi.org/10.2210/pdb3LV9/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-19 Released: 2010-03-09
Deposition Author(s): Nocek, B., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.262 (Depositor), 0.266 (DCC)
R-Value Work:
0.201 (Depositor), 0.211 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LV9

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

Literature

Crystal structure of CBS domain of a putative transporter from Clostridium difficile 630

Nocek, B., Tesar, C., Cobb, G., Joachimiak, A., MCSG

To be published.

Macromolecule Content

Total Structure Weight: 17.41 kDa
Atom Count: 1,074
Modeled Residue Count: 130
Deposited Residue Count: 148
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transporter	A	148	Clostridioides difficile 630	Mutation(s): 0
UniProt
Find proteins for Q183U2 (Clostridioides difficile (strain 630)) Explore Q183U2 Go to UniProtKB: Q183U2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q183U2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.262 (Depositor), 0.266 (DCC)
R-Value Work: 0.201 (Depositor), 0.211 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.641	α = 90
b = 43.641	β = 90
c = 127.763	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
MLPHARE	phasing
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-10-09
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.