9BUF | pdb_00009buf

Hydrolase domain of Chitinase 1 from Streptomyces venezuelae

PDB DOI: https://doi.org/10.2210/pdb9BUF/pdb

Classification: HYDROLASE
Organism(s): Streptomyces venezuelae ATCC 10712
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-17 Released: 2025-08-27
Deposition Author(s): Dalton, J.A.T., Smith, O.B., Frkic, R.L., Jackson, C.J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.232 (Depositor), 0.229 (DCC)
R-Value Work:
0.195 (Depositor), 0.191 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9BUF

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

Literature

Hydrolase domain of Chitinase 1 from Streptomyces venezuelae

Dalton, J.A.T., Smith, O.B., Frkic, R.L., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 65.56 kDa
Atom Count: 4,893
Modeled Residue Count: 591
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exochitinase 1	A, B	315	Streptomyces venezuelae ATCC 10712	Mutation(s): 0 Gene Names: SVEN_2589 EC: 3.2.1.14
UniProt
Find proteins for F2R3N3 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)) Explore F2R3N3 Go to UniProtKB: F2R3N3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2R3N3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.232 (Depositor), 0.229 (DCC)
R-Value Work: 0.195 (Depositor), 0.191 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.529	α = 90
b = 54.769	β = 92.13
c = 144.421	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

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: 2025-08-27
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.