4L4O | pdb_00004l4o

The crystal structure of CbXyn10B in native form

PDB DOI: https://doi.org/10.2210/pdb4L4O/pdb

Classification: HYDROLASE
Organism(s): Caldicellulosiruptor bescii DSM 6725
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-08 Released: 2014-05-07
Deposition Author(s): An, J., Feng, Y., Wu, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.236 (Depositor), 0.268 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of CbXyn10B from Caldicellulosiruptor bescii and its mutant(E139A) in complex with xylotriose

An, J., Feng, Y., Wu, G.

To be published.

Macromolecule Content

Total Structure Weight: 41.45 kDa
Atom Count: 2,871
Modeled Residue Count: 330
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	345	Caldicellulosiruptor bescii DSM 6725	Mutation(s): 0 Gene Names: Athe_0185 EC: 3.2.1.8
UniProt
Find proteins for B9MMA5 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320)) Explore B9MMA5 Go to UniProtKB: B9MMA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9MMA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
144 Query on 144 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]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C₄ H₁₂ N O₃ DRDCQJADRSJFFD-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: 2.05 Å
R-Value Free: 0.236 (Depositor), 0.268 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.701	α = 90
b = 78.801	β = 90
c = 115.959	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.