2YV5 | pdb_00002yv5

Crystal structure of Yjeq from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2YV5/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-04-09 Released: 2008-04-15 
• Deposition Author(s): Wang, H., Kaminishi, T., Hanawa-Suetsugu, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YjeQ from Aquifex aeolicus

Wang, H., Kaminishi, T., Hanawa-Suetsugu, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S.

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: 35.34 kDa 
• Atom Count: 2,615 
• Modeled Residue Count: 293 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YjeQ protein	A	302	Aquifex aeolicus	Mutation(s): 0  Gene Names: YjeQ EC: 3.6.1
UniProt
Find proteins for O66555 (Aquifex aeolicus (strain VF5)) Explore O66555  Go to UniProtKB:  O66555

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.139	α = 90
b = 63.139	β = 90
c = 157.319	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Wang, H., Kaminishi, T., Hanawa-Suetsugu, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary