3ME1 | pdb_00003me1

Crystal Structure of the Desulfovibro vulgaris Urea Transporter in the P3(1) Space Group at 3.86

PDB DOI: https://doi.org/10.2210/pdb3ME1/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2010-03-31 Released: 2011-01-19
Deposition Author(s): Levin, E.J., Zhou, M., New York Consortium on Membrane Protein Structure (NYCOMPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.86 Å
R-Value Free:
0.387 (Depositor), 0.388 (DCC)
R-Value Work:
0.321 (Depositor), 0.317 (DCC)
R-Value Observed:
0.324 (Depositor)

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

Literature

Crystal Structure of the Desulfovibro vulgaris Urea Transporter in the P3(1) Space Group at 3.86 .

Levin, E.J., Zhou, M.

To be published.

Macromolecule Content

Total Structure Weight: 106.48 kDa
Atom Count: 4,673
Modeled Residue Count: 956
Deposited Residue Count: 1,005
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea transporter	A, B, C	335	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 Gene Names: DVU_1160 Membrane Entity: Yes
UniProt
Find proteins for Q72CX3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72CX3 Go to UniProtKB: Q72CX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72CX3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.86 Å
R-Value Free: 0.387 (Depositor), 0.388 (DCC)
R-Value Work: 0.321 (Depositor), 0.317 (DCC)
R-Value Observed: 0.324 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.197	α = 90
b = 103.197	β = 90
c = 141.498	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

New York Consortium on Membrane Protein Structure (NYCOMPS)

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, 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.