2BDZ | pdb_00002bdz

Mexicain from Jacaratia mexicana

• PDB DOI: https://doi.org/10.2210/pdb2BDZ/pdb

• Classification: HYDROLASE
• Organism(s): Jacaratia mexicana
• Mutation(s): No 


• Deposited: 2005-10-21 Released: 2006-10-03 
• Deposition Author(s): Gavira, J.A., Oliver-Salvador, M.C., Gonzalez-Ramirez, L.A., Soriano-Garcia, M., Garcia-Ruiz, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.181 (DCC) 

Starting Models: experimental

Literature

Crystallographic structure of Mexicain from Jacaratia mexicana

Gavira, J.A., Oliver-Salvador, M.C., Gonzalez-Ramirez, L.A., Soriano-Garcia, M., Garcia-Ruiz, J.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.62 kDa 
• Atom Count: 7,002 
• Modeled Residue Count: 848 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mexicain	A, B, C, D	214	Jacaratia mexicana	Mutation(s): 0  EC: 3.4.22
UniProt
Find proteins for P84346 (Jacaratia mexicana) Explore P84346  Go to UniProtKB:  P84346

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64	E [auth A], F [auth B], G [auth C], H [auth D]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.181 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.356	α = 90
b = 90.454	β = 92.636
c = 80.391	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Gavira, J.A., Oliver-Salvador, M.C., Gonzalez-Ramirez, L.A., Soriano-Garcia, M., Garcia-Ruiz, J.M.

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary