1H4G

Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre

PDB DOI: https://doi.org/10.2210/pdb1H4G/pdb

Classification: GLYCOSIDE HYDROLASE
Organism(s): Salipaludibacillus agaradhaerens
Expression System: Bacillus licheniformis
Mutation(s): Yes

Deposited: 2001-05-11 Released: 2002-05-09
Deposition Author(s): Sabini, E., Wilson, K.S., Danielsen, S., Schulein, M., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.181
R-Value Work: 0.158

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 47.17 kDa
Atom Count: 3,970
Modelled Residue Count: 413
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XYLANASE	A, B	207	Salipaludibacillus agaradhaerens	Mutation(s): 1 EC: 3.2.1.8
UniProt
Find proteins for Q7SIE3 (Salipaludibacillus agaradhaerens) Explore Q7SIE3 Go to UniProtKB: Q7SIE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SIE3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-2-deoxy-2-fluoro-alpha-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: G53360CN GlyCosmos: G53360CN

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 E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B]	E [auth A], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.181
R-Value Work: 0.158
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.061	α = 90
b = 75.098	β = 90
c = 78.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-05-09
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations
Version 2.0: 2020-03-11
Changes: Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary

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Help and Resources

1H4G

Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)