1ZS7 | pdb_00001zs7

The structure of gene product APE0525 from Aeropyrum pernix

• PDB DOI: https://doi.org/10.2210/pdb1ZS7/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-05-23 Released: 2005-07-05 
• Deposition Author(s): Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.199 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

The structure of gene product APE0525 from Aeropyrum pernix

Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.76 kDa 
• Atom Count: 1,790 
• Modeled Residue Count: 187 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein APE0525	A	190	Aeropyrum pernix K1	Mutation(s): 3  Gene Names: APE0525
UniProt
Find proteins for Q9YEQ6 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YEQ6  Go to UniProtKB:  Q9YEQ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.199 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.85	α = 90
b = 112.792	β = 90
c = 39.001	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-05 
Deposition Author(s): Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2014-04-16
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary