5HNN | pdb_00005hnn

Crystal structure of the endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg.

PDB DOI: https://doi.org/10.2210/pdb5HNN/pdb

Classification: HYDROLASE
Organism(s): Xanthomonas citri subsp. citri 306
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2016-01-18 Released: 2017-01-25
Deposition Author(s): Paiva, J.H., Murakami, M.T.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.198 (Depositor), 0.201 (DCC)
R-Value Work:
0.146 (Depositor)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg.

Paiva, J.H., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 111.99 kDa
Atom Count: 8,050
Modeled Residue Count: 948
Deposited Residue Count: 1,011
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase	A, B, C	337	Xanthomonas citri subsp. citri 306	Mutation(s): 3 Gene Names: egl, XAC0030

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.198 (Depositor), 0.201 (DCC)
R-Value Work: 0.146 (Depositor)
R-Value Observed: 0.149 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.554	α = 90
b = 76.87	β = 98.7
c = 128.942	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/13309-0 and 2014/07135-1

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-09
Changes: 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.