1YIF | pdb_00001yif

CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

PDB DOI: https://doi.org/10.2210/pdb1YIF/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-01-11 Released: 2005-01-18
Deposition Author(s): Patskovsky, Y., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.205 (Depositor), 0.200 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS

Patskovsky, Y., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 245.63 kDa
Atom Count: 20,084
Modeled Residue Count: 2,128
Deposited Residue Count: 2,132
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-1,4-XYLOSIDASE	A, B, C, D	533	Bacillus subtilis	Mutation(s): 0 Gene Names: XYNB EC: 3.2.1.37
UniProt
Find proteins for P94489 (Bacillus subtilis (strain 168)) Explore P94489 Go to UniProtKB: P94489
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P94489
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.205 (Depositor), 0.200 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.23	α = 90
b = 104.61	β = 108.88
c = 114.6	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
ARP/wARP	model building
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-01-18

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2005-01-18
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: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-02-03
Changes: Structure summary
Version 1.5: 2024-02-14
Changes: Data collection, Database references

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.