2YWF | pdb_00002ywf

Crystal structure of GMPPNP-bound LepA from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2YWF/pdb

• Classification: TRANSLATION
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-20 Released: 2008-04-29 
• Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of GTP-binding protein LepA from Aquifex aeolicus

Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., 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: 68.3 kDa 
• Atom Count: 4,438 
• Modelled Residue Count: 532 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein lepA	A	600	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: lepA
UniProt
Find proteins for O67618 (Aquifex aeolicus (strain VF5)) Explore O67618  Go to UniProtKB:  O67618

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.451	α = 90
b = 116.142	β = 90
c = 123.329	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description