3BRS | pdb_00003brs

Crystal structure of sugar transporter from Clostridium phytofermentans

PDB DOI: https://doi.org/10.2210/pdb3BRS/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Lachnoclostridium phytofermentans ISDg
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-21 Released: 2008-02-05
Deposition Author(s): Malashkevich, V.N., Patskovsky, Y., Toro, R., Meyers, A.J., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.283 (Depositor), 0.288 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of sugar transporter from Clostridium phytofermentans.

Malashkevich, V.N., Patskovsky, Y., Toro, R., Meyers, A.J., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 64.66 kDa
Atom Count: 4,477
Modeled Residue Count: 542
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A, B	289	Lachnoclostridium phytofermentans ISDg	Mutation(s): 0 Gene Names: CphyDRAFT_2568
UniProt
Find proteins for A9KIC5 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)) Explore A9KIC5 Go to UniProtKB: A9KIC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9KIC5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.283 (Depositor), 0.288 (DCC)
R-Value Work: 0.203 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.62	α = 90
b = 54.7	β = 111.78
c = 90.24	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-05

Deposition Author(s):

Malashkevich, V.N.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-02-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references

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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.