5EBA | pdb_00005eba

Crystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27

PDB DOI: https://doi.org/10.2210/pdb5EBA/pdb

Classification: HYDROLASE
Organism(s): Bacillus sp. NG-27
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-10-18 Released: 2016-10-19
Deposition Author(s): Mahanta, P., Bhardwaj, A., Reddy, V.S., Ramakumar, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.235 (Depositor)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27

Mahanta, P., Bhardwaj, A., Reddy, V.S., Ramakumar, S.

To be published.

Macromolecule Content

Total Structure Weight: 41.07 kDa
Atom Count: 3,053
Modeled Residue Count: 354
Deposited Residue Count: 355
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A	355	Bacillus sp. NG-27	Mutation(s): 1 EC: 3.2.1.8
UniProt
Find proteins for O30700 (Bacillus sp. NG-27) Explore O30700 Go to UniProtKB: O30700
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O30700
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.235 (Depositor)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.86	α = 90
b = 80.11	β = 111.19
c = 69.21	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-19
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.