1WCX | pdb_00001wcx

Crystal Structure of Mutant Uroporphyrinogen III Synthase from an Extremely Thermophilic Bacterium Thermus thermophilus HB8 (L75M/I193M/L248M, SeMet derivative, Form-1 crystal)

• PDB DOI: https://doi.org/10.2210/pdb1WCX/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-05-06 Released: 2005-05-06 
• Deposition Author(s): Mizohata, E., Matsuura, T., Murayama, K., Sakai, H., Terada, T., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal Structure of Uroporphyrinogen III Synthase from Thermus thermophilus HB8

Mizohata, E., Matsuura, T., Murayama, K., Sakai, H., Terada, T., Shirouzu, M., Kuramitsu, S., Yokoyama, 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: 28.82 kDa 
• Atom Count: 2,108 
• Modeled Residue Count: 252 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen III Synthase	A	261	Thermus thermophilus	Mutation(s): 4  EC: 4.2.1.75
UniProt
Find proteins for Q5SKH2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKH2  Go to UniProtKB:  Q5SKH2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.548	α = 90
b = 66.105	β = 91.4
c = 55.857	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-06 
Deposition Author(s): Mizohata, E., Matsuura, T., Murayama, K., Sakai, H., Terada, T., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-05-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary