2NQY | pdb_00002nqy

Crystal structure of alkaline thermophlic xylanase from Bacillus sp. (NCL 86-6-10) with complex xylotriose: Xylotriose cleaved to xylobiose and xylose

PDB DOI: https://doi.org/10.2210/pdb2NQY/pdb

Classification: HYDROLASE
Organism(s): Bacillus sp. (in: firmicutes)
Mutation(s): No

Deposited: 2006-11-01 Released: 2007-11-06
Deposition Author(s): Satyanarayana, L., Gaikwad, S.M., Balakrishnan, H., Suresh, C.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.243 (Depositor), 0.231 (DCC)
R-Value Work:
0.192 (Depositor), 0.187 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of alkaline thermophlic xylanase from Bacillus sp. (NCL 86-6-10) with complex xylotriose: Xylotriose cleaved to xylobiose and xylose

Satyanarayana, L., Gaikwad, S.M., Balakrishnan, H., Suresh, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 46.32 kDa
Atom Count: 3,402
Modeled Residue Count: 412
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAMILY 11 XYLANASE	A, B	206	Bacillus sp. (in: firmicutes)	Mutation(s): 0 EC: 3.2.1.8
UniProt
Find proteins for Q7SIE3 (Salipaludibacillus agaradhaerens) Explore Q7SIE3 Go to UniProtKB: Q7SIE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIE3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP Query on XYP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

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	C, D	4beta-beta-xylobiose	Oligosaccharide / Metabolism		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.243 (Depositor), 0.231 (DCC)
R-Value Work: 0.192 (Depositor), 0.187 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.363	α = 90
b = 78.363	β = 90
c = 140.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-12-20
Changes: Advisory, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary