2PG4

Crystal structure of a putative dna binding protein (ape_0880a) from aeropyrum pernix k1 at 2.21 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PG4/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-06 Released: 2007-04-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.258 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Crystal structure of uncharacterized protein (NP_147569.1) from Aeropyrum pernix at 2.21 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.69 kDa 
• Atom Count: 1,591 
• Modelled Residue Count: 183 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	95	Aeropyrum pernix K1	Mutation(s): 2  Gene Names: NP_147569.1, APE0880.1, APES039, APE_0880a
UniProt
Find proteins for Q9YDN4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YDN4  Go to UniProtKB:  Q9YDN4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	K [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG	N [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.258 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 4 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M32PG4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.84	α = 90
b = 109.84	β = 90
c = 36.76	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations