4Q4L | pdb_00004q4l

Crystal structure of an ATP synthase subunit beta 1 (F1-B1) from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb4Q4L/pdb

Classification: HYDROLASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-04-14 Released: 2014-04-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.236 (Depositor), 0.233 (DCC)
R-Value Work:
0.194 (Depositor), 0.201 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an ATP synthase subunit beta 1 (F1-B1) from Burkholderia thailandensis

Edwards, T.E., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 52.99 kDa
Atom Count: 3,325
Modeled Residue Count: 436
Deposited Residue Count: 485
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta 1	A	485	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: aptD1, atpD1, BTH_I3308 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for Q2STE9 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2STE9 Go to UniProtKB: Q2STE9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2STE9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236 (Depositor), 0.233 (DCC)
R-Value Work: 0.194 (Depositor), 0.201 (DCC)
R-Value Observed: 0.196 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.42	α = 90
b = 97.99	β = 90
c = 127.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2025-10-22
Changes: 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.