4W5Z | pdb_00004w5z

High resolution crystal structure of catalytic domain of Chitinase 60 from psychrophilic bacteria Moritella marina.

PDB DOI: https://doi.org/10.2210/pdb4W5Z/pdb

Classification: HYDROLASE
Organism(s): Moritella marina
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-19 Released: 2015-08-26
Deposition Author(s): Malecki, P.H., Vorgias, C.E., Rypniewski, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.150 (Depositor), 0.150 (DCC)
R-Value Work:
0.111 (Depositor), 0.110 (DCC)
R-Value Observed:
0.111 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

High resolution crystal structure of catalytic domain of Chitinase 60 from psychrophilic bacteria Moritella marina.

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

To be published.

Macromolecule Content

Total Structure Weight: 38.9 kDa
Atom Count: 3,056
Modeled Residue Count: 323
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase 60	A	345	Moritella marina	Mutation(s): 0 Gene Names: chi60 EC: 3.2.1.14
UniProt
Find proteins for B1VBB0 (Moritella marina) Explore B1VBB0 Go to UniProtKB: B1VBB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1VBB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD 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]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth A] mmCIF format, chain K [auth A] mmCIF format, chain E [auth A]	E [auth A], K [auth A], N [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth A] Focus chain N [auth A] Interactions & Density Focus chain E [auth A] Focus chain K [auth A] Focus chain N [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A] D [auth A] F [auth A] G [auth A] H [auth A] B [auth A], D [auth A], F [auth A], G [auth A], H [auth A], L [auth A], M [auth A], O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.150 (Depositor), 0.150 (DCC)
R-Value Work: 0.111 (Depositor), 0.110 (DCC)
R-Value Observed: 0.111 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.691	α = 90
b = 72.686	β = 90
c = 171.169	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Malecki, P.H.

Vorgias, C.E.

Rypniewski, W.

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

Revision History (Full details and data files)

Version 1.0: 2015-08-26
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary