9OJL | pdb_00009ojl

Crystal Structure of GH18 Chitinase Domain from Vibrio splendidus

PDB DOI: https://doi.org/10.2210/pdb9OJL/pdb

Classification: HYDROLASE
Organism(s): Vibrio splendidus
Expression System: Vibrio natriegens
Mutation(s): No

Deposited: 2025-05-08 Released: 2025-05-21
Deposition Author(s): Horton, J.G., Jackson, C.J., Frkic, R.L.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.169 (Depositor), 0.167 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9OJL

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of GH18 Chitinase Domain from Vibrio splendidus

Horton, J.G., Jackson, C.J., Frkic, R.L.

To be published.

Macromolecule Content

Total Structure Weight: 226.85 kDa
Atom Count: 17,698
Modeled Residue Count: 1,909
Deposited Residue Count: 2,016
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A, B, C, D, E A, B, C, D, E, F	336	Vibrio splendidus	Mutation(s): 0 Gene Names: AN168_05695
UniProt
Find proteins for A0A837NXJ2 (Vibrio splendidus) Explore A0A837NXJ2 Go to UniProtKB: A0A837NXJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A837NXJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B], R [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain CA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth E]	CA [auth E], H [auth A], L [auth B], Q [auth C], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth E] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain Y [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain GA [auth F] SDF format, chain G [auth A] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain DA [auth E] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] DA [auth E] EA [auth F] FA [auth F] AA [auth D], BA [auth D], DA [auth E], EA [auth F], FA [auth F], G [auth A], GA [auth F], I [auth A], K [auth A], M [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.210 (Depositor), 0.209 (DCC)
R-Value Work: 0.169 (Depositor), 0.167 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.918	α = 90
b = 154.033	β = 90
c = 156.602	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE200100012
Australian Research Council (ARC)	Australia	CE200100029

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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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.