2P17 | pdb_00002p17

Crystal structure of GK1651 from Geobacillus kaustophilus

• PDB DOI: https://doi.org/10.2210/pdb2P17/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-02 Released: 2007-05-01 
• Deposition Author(s): Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of GK1651 from Geobacillus kaustophilus

Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.C.

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: 31.52 kDa 
• Atom Count: 2,163 
• Modeled Residue Count: 249 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin-like protein	A	277	Geobacillus kaustophilus HTA426	Mutation(s): 9  Gene Names: GK1651
UniProt
Find proteins for Q5KZF0 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KZF0  Go to UniProtKB:  Q5KZF0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-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: 1.52 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.571	α = 90
b = 59.823	β = 90
c = 69.685	γ = 90

Software Package:

Software Name	Purpose
SGXPRO	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SGXPRO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-09-13
  Changes: Advisory, Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2024-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary