2RKH | pdb_00002rkh

Crystal structure of a putative AphA-like transcription factor (ZP_00208345.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RKH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Paramagnetospirillum magnetotacticum MS-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-16 Released: 2007-10-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of a putative AphA-like transcription factor (ZP_00208345.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 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 Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 20.11 kDa 
• Atom Count: 1,292 
• Modeled Residue Count: 164 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative AphA-like transcription factor	A	180	Paramagnetospirillum magnetotacticum MS-1	Mutation(s): 0  Gene Names: ZP_00208345.1

Small Molecules

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: 2.00 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32RKH

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.62	α = 90
b = 66.62	β = 90
c = 92.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary