3WYN | pdb_00003wyn

Structure of calcium bound cutinase Est119 from Thermobifida alba.

• PDB DOI: https://doi.org/10.2210/pdb3WYN/pdb

• Classification: HYDROLASE
• Organism(s): Thermobifida alba
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-02 Released: 2014-09-24 
• Deposition Author(s): Kitadokoro, K., Thumarat, U., Kawai, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of calcium bound cutinase Est119 from Thermobifida alba.

Kitadokoro, K., Thumarat, U., Kawai, F.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.97 kDa 
• Atom Count: 4,464 
• Modeled Residue Count: 521 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B	306	Thermobifida alba	Mutation(s): 0  Gene Names: est2 EC: 3.1.1.101 (UniProt), 3.1.1.74 (UniProt)
UniProt
Find proteins for F7IX06 (Thermobifida alba) Explore F7IX06  Go to UniProtKB:  F7IX06

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	D [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
CA	C [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.473	α = 90
b = 87.74	β = 133.35
c = 72.619	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Kitadokoro, K., Thumarat, U., Kawai, F.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary