4TX8 | pdb_00004tx8

Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum

PDB DOI: https://doi.org/10.2210/pdb4TX8/pdb

Classification: HYDROLASE
Organism(s): Chromobacterium violaceum ATCC 12472
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2014-07-02 Released: 2015-10-14
Deposition Author(s): Pereira, H.M., Lobo, M.D.P., Brandao-Neto, J., Grangeiro, T.B.
Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq), Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum

Pereira, H.M., Lobo, M.D.P., Brandao-Neto, J., Grangeiro, T.B.

To be published.

Macromolecule Content

Total Structure Weight: 46.8 kDa
Atom Count: 3,133
Modeled Residue Count: 374
Deposited Residue Count: 439
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable chitinase A	A	439	Chromobacterium violaceum ATCC 12472	Mutation(s): 0 Gene Names: CV_2935 EC: 3.2.1.14
UniProt
Find proteins for Q7NTW8 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NTW8 Go to UniProtKB: Q7NTW8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NTW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.17 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.48	α = 90
b = 120.48	β = 90
c = 106.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
xia2	data scaling
PHASER	phasing
GDA	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	--
Sao Paulo Research Foundation (FAPESP)	Brazil	--

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Data collection, Derived calculations, Refinement description
Version 1.2: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-11-13
Changes: Structure summary