1UFV | pdb_00001ufv

Crystal Structure Of Pantothenate Synthetase From Thermus Thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1UFV/pdb

• Classification: LIGASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-06-10 Released: 2003-06-24 
• Deposition Author(s): Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.246 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Crystal Structure Of Pantothenate Synthetase From Thermus Thermophilus HB8

Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H.

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 PQS (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.45 kDa 
• Atom Count: 4,852 
• Modeled Residue Count: 552 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantoate-beta-alanine ligase	A, B	276	Thermus thermophilus	Mutation(s): 0  Gene Names: PanC EC: 6.3.2.1
UniProt
Find proteins for Q5SHF5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHF5  Go to UniProtKB:  Q5SHF5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A], I [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: 2.05 Å
• R-Value Free:  0.246 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.197 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.558	α = 90
b = 88.558	β = 90
c = 266.974	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-24 
Deposition Author(s): Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary