7VME | pdb_00007vme

Crystal structure of a hydrolase in apo form 2

• PDB DOI: https://doi.org/10.2210/pdb7VME/pdb

• Classification: HYDROLASE
• Organism(s): unclassified Marinobacter
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-08 Released: 2022-10-12 
• Deposition Author(s): Wu, P., Zhao, Y.P., Li, Z.S., Ingrid, M.C., Lara, P., Gao, J., Han, X., Li, Q., Basak, O., Liu, W.D., Wei, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a hydrolase in apo form 2

Wu, P., Zhao, Y.P., Li, Z.S., Ingrid, M.C., Lara, P., Gao, J., Han, X., Li, Q., Basak, O., Liu, W.D., Wei, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 31.31 kDa 
• Atom Count: 2,296 
• Modeled Residue Count: 266 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydrolase	A	293	unclassified Marinobacter	Mutation(s): 0
UniProt
Find proteins for A0A9X9ZA41 (unclassified Marinobacter) Explore A0A9X9ZA41  Go to UniProtKB:  A0A9X9ZA41

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.7	α = 90
b = 65.954	β = 90
c = 82.885	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Wu, P., Zhao, Y.P., Li, Z.S., Ingrid, M.C., Lara, P., Gao, J., Han, X., Li, Q., Basak, O., Liu, W.D., Wei, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary