4PMD | pdb_00004pmd

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

PDB DOI: https://doi.org/10.2210/pdb4PMD/pdb

Classification: HYDROLASE
Organism(s): Caldicellulosiruptor bescii DSM 6725
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-05-21 Released: 2015-06-24
Deposition Author(s): An, J., Feng, Y., Wu, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.212 (Depositor), 0.254 (DCC)
R-Value Work:
0.192 (Depositor)
R-Value Observed:
0.193 (Depositor)

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This is version 2.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 40.59 kDa
Atom Count: 2,938
Modeled Residue Count: 329
Deposited Residue Count: 338
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	338	Caldicellulosiruptor bescii DSM 6725	Mutation(s): 1 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

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G87728WL GlyCosmos: G87728WL

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116 Query on PRD_900116	B	4beta-beta-xylobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.212 (Depositor), 0.254 (DCC)
R-Value Work: 0.192 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.319	α = 90
b = 80.817	β = 90
c = 115.19	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
Version 2.1: 2024-03-20
Changes: Data collection, 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.