4C45 | pdb_00004c45

Crystal structure of human pterin-4-alpha-carbinolamine dehydratase 2 (PCBD2)

• PDB DOI: https://doi.org/10.2210/pdb4C45/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-30 Released: 2013-09-11 
• Deposition Author(s): Kopec, J., Kiyani, W., Vollmar, M., Shrestha, L., Canning, P., von Delft, F., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Pterin-4-Alpha- Carbinolamine Dehydratase 2 (Pcbd2)

Kopec, J., Kiyani, W., Vollmar, M., Shrestha, L., Canning, P., von Delft, F., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.93 kDa 
• Atom Count: 908 
• Modelled Residue Count: 99 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE 2	A	104	Homo sapiens	Mutation(s): 0  EC: 4.2.1.96
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0N5 (Homo sapiens) Explore Q9H0N5  Go to UniProtKB:  Q9H0N5
PHAROS:  Q9H0N5 GTEx:  ENSG00000132570

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.547	α = 90
b = 94.044	β = 90
c = 48.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Kopec, J., Kiyani, W., Vollmar, M., Shrestha, L., Canning, P., von Delft, F., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W.W.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description