4W5U | pdb_00004w5u

Crystal structure of chitinase 40 from thermophilic bacteria Streptomyces thermoviolaceus.

PDB DOI: https://doi.org/10.2210/pdb4W5U/pdb

Classification: HYDROLASE
Organism(s): Streptomyces thermoviolaceus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-18 Released: 2015-08-26
Deposition Author(s): Malecki, P.H., Vorgias, C.E., Rypniewski, W.
Funding Organization(s): The project was co-funded by the European Union within the European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.150 (Depositor), 0.157 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 4W5U

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

Literature

The Crystal Structure of a Streptomyces thermoviolaceus Thermophilic Chitinase Known for Its Refolding Efficiency

Malecki, P.H., Bejger, M., Rypniewski, W., Vorgias, C.E.

(2020) Int J Mol Sci

DOI: https://doi.org/10.3390/ijms21082892

Macromolecule Content

Total Structure Weight: 86.87 kDa
Atom Count: 5,660
Modeled Residue Count: 739
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A [auth B], B [auth A]	408	Streptomyces thermoviolaceus	Mutation(s): 0 Gene Names: chi40 EC: 3.2.1.14
UniProt
Find proteins for Q56077 (Streptomyces thermoviolaceus) Explore Q56077 Go to UniProtKB: Q56077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56077
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.208 (Depositor), 0.210 (DCC)
R-Value Work: 0.150 (Depositor), 0.157 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.15	α = 90
b = 183.15	β = 90
c = 130.814	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
Aimless	data scaling
XSCALE	data scaling
XSCALE	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
The project was co-funded by the European Union within the European Regional Development Fund	Poland	--

Revision History (Full details and data files)

Version 1.0: 2015-08-26
Type: Initial release
Version 1.1: 2018-01-17
Changes: Data collection
Version 2.0: 2020-04-29
Changes: Atomic model, Database references
Version 2.1: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-11-06
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.