7VLZ | pdb_00007vlz

Crystal structure of the collagenase unit of a Vibrio collagenase from Vibrio harveyi VHJR7

• PDB DOI: https://doi.org/10.2210/pdb7VLZ/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio harveyi VHJR7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-05 Released: 2022-10-19 
• Deposition Author(s): Cao, H.Y., Wang, Y., Peng, M., Zhang, Y.Z.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the collagenase unit of a Vibrio collagenase from Vibrio harveyi VHJR7

Wang, Y., Cao, H.Y., Peng, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.16 kDa 
• Atom Count: 5,363 
• Modeled Residue Count: 558 
• Deposited Residue Count: 639 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
collagenase	A	613	Vibrio harveyi VHJR7	Mutation(s): 0  EC: 3.4.24.3
UniProt
Find proteins for A0A8B3DGT3 (Vibrio harveyi) Explore A0A8B3DGT3  Go to UniProtKB:  A0A8B3DGT3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide P1	B	14	Vibrio harveyi VHJR7	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide P2	C	12	Vibrio harveyi VHJR7	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.641	α = 90
b = 50.573	β = 104.98
c = 90.968	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Cao, H.Y., Wang, Y., Peng, M., Zhang, Y.Z.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	U2006205
National Science Foundation (NSF, China)	China	U1706207

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary