3HV1 | pdb_00003hv1

Crystal structure of a polar amino acid ABC uptake transporter substrate binding protein from Streptococcus thermophilus

PDB DOI: https://doi.org/10.2210/pdb3HV1/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-15 Released: 2009-06-23
Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3HV1

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

Literature

Crystal structure of a polar amino acid ABC uptake transporter substrate binding protein from Streptococcus thermophilus

Palani, K., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 61.01 kDa
Atom Count: 4,391
Modeled Residue Count: 518
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polar amino acid ABC uptake transporter substrate binding protein	A, B	268	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: stu0877
UniProt
Find proteins for Q5M4P7 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4P7 Go to UniProtKB: Q5M4P7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M4P7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.254 (Depositor), 0.253 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.559	α = 90
b = 78.563	β = 105.41
c = 80.03	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, 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.