2B46 | pdb_00002b46

Crystal structure of an engineered uninhibited Bacillus subtilis xylanase in substrate bound state

PDB DOI: https://doi.org/10.2210/pdb2B46/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-09-22 Released: 2006-09-19
Deposition Author(s): Sansen, S., Dewilde, M., De Ranter, C.J., Sorensen, J.F., Sibbesen, O., Gebruers, K., Brijs, K., Courtin, C.M., Delcour, J.A., Rabijns, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.198 (Depositor), 0.206 (DCC)
R-Value Work:
0.169 (Depositor), 0.177 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the Triticum xylanse inhibitor-I in complex with bacillus subtilis xylanase

Sansen, S., Dewilde, M., De Ranter, C.J., Gebruers, K., Brijs, K., Courtin, C.M., Delcour, J.A., Rabijns, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.67 kDa
Atom Count: 1,541
Modeled Residue Count: 185
Deposited Residue Count: 185
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase A	A [auth X]	185	Bacillus subtilis	Mutation(s): 2 Gene Names: xynA EC: 3.2.1.8
UniProt
Find proteins for P18429 (Bacillus subtilis (strain 168)) Explore P18429 Go to UniProtKB: P18429
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18429
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B [auth A]	2		N/A	Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
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 [auth A]	4beta-beta-xylobiose	Oligosaccharide / Metabolism		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.198 (Depositor), 0.206 (DCC)
R-Value Work: 0.169 (Depositor), 0.177 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.653	α = 90
b = 60.653	β = 90
c = 95.513	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-09-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-19
Type: Initial release
Version 1.1: 2008-05-01
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, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Derived calculations, Structure summary
Version 2.2: 2024-02-14
Changes: Data collection