1YAV | pdb_00001yav

Crystal structure of CBS domain-containing protein ykuL from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1YAV/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-12-17 Released: 2004-12-28
Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YAV

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of a hypothetical protein (ykul) containing CBS domains from Bacillus subtilis.

Kumaran, D., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.12 kDa
Atom Count: 2,208
Modeled Residue Count: 269
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein BSU14130	A, B	159	Bacillus subtilis	Mutation(s): 0 Gene Names: ykuL
UniProt
Find proteins for O31698 (Bacillus subtilis (strain 168)) Explore O31698 Go to UniProtKB: O31698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.262 (Depositor), 0.263 (DCC)
R-Value Work: 0.228 (Depositor), 0.229 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.564	α = 90
b = 69.592	β = 90
c = 70.903	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-12-28

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-12-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-14
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.