3BF5 | pdb_00003bf5

Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BF5/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma acidophilum DSM 1728
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-20 Released: 2007-12-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.92 kDa 
• Atom Count: 4,673 
• Modeled Residue Count: 563 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase related protein	A, B	306	Thermoplasma acidophilum DSM 1728	Mutation(s): 3  Gene Names: 10640157, Ta0880 EC: 2.7.1.213 (UniProt), 2.7.1.20 (UniProt), 2.7.1.73 (UniProt)
UniProt
Find proteins for Q9HJT3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJT3  Go to UniProtKB:  Q9HJT3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
PGO	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

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: 1.91 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33BF5

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.45	α = 90
b = 59.18	β = 90
c = 177.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-01-25
  Changes: Database references
• Version 1.6: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary