1WKC | pdb_00001wkc

Crystal structure of a 5-formyltetrahydrofolate cycloligase-related protein from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1WKC/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-31 Released: 2004-12-01 
• Deposition Author(s): Yanai, H., Tsuge, H., Utsunomiya, H., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.251 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal structure of a 5-formyltetrahydrofolate cycloligase-related protein from Thermus thermophilus HB8

Yanai, H., Tsuge, H., Utsunomiya, H., Yokoyama, S., Kuramitsu, S.

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: 20.84 kDa 
• Atom Count: 1,504 
• Modeled Residue Count: 168 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HB8 TT1367 protein	A	184	Thermus thermophilus HB8	Mutation(s): 2  EC: 6.3.3.2
UniProt
Find proteins for Q5SHW9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHW9  Go to UniProtKB:  Q5SHW9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.70 Å
• R-Value Free:  0.251 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.01	α = 90
b = 73.37	β = 90
c = 107.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-01 
Deposition Author(s): Yanai, H., Tsuge, H., Utsunomiya, H., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-12-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary