1VCI | pdb_00001vci

Crystal structure of the ATP-binding cassette of multisugar transporter from Pyrococcus horikoshii OT3 complexed with ATP

PDB DOI: https://doi.org/10.2210/pdb1VCI/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2004-03-08 Released: 2004-12-14
Deposition Author(s): Ose, T., Fujie, T., Yao, M., Watanabe, N., Tanaka, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.297 (Depositor), 0.285 (DCC)
R-Value Work:
0.215 (Depositor), 0.203 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the ATP-binding cassette of multisugar transporter from Pyrococcus horikoshii OT3

Ose, T., Fujie, T., Yao, M., Watanabe, N., Tanaka, I.

(2004) Proteins 57: 635-638

PubMed: 15382245 Search on PubMed
DOI: https://doi.org/10.1002/prot.20206
Primary Citation Related Structures:
1V43, 1VCI

Organizational Affiliation

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan.

Macromolecule Content

Total Structure Weight: 42.63 kDa
Atom Count: 2,914
Modeled Residue Count: 353
Deposited Residue Count: 373
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sugar-binding transport ATP-binding protein	A	373	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH0022
UniProt
Find proteins for O57758 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57758 Go to UniProtKB: O57758
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O57758
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.297 (Depositor), 0.285 (DCC)
R-Value Work: 0.215 (Depositor), 0.203 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.84	α = 90
b = 79.84	β = 90
c = 130.08	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-12-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-12-14
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, 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.