6IUQ | pdb_00006iuq

Crystal structure and expression patterns of prolyl 4-hydroxylases from Phytophthora capsici

• PDB DOI: https://doi.org/10.2210/pdb6IUQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phytophthora capsici LT1534
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-29 Released: 2018-12-12 
• Deposition Author(s): Song, W.W., Zhang, X.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.217 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure and expression patterns of prolyl 4-hydroxylases from Phytophthora capsici

Song, W.W., Zhang, X.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.07 kDa 
• Atom Count: 5,095 
• Modeled Residue Count: 591 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl 4-hydroxylase	A, B	345	Phytophthora capsici LT1534	Mutation(s): 0
UniProt
Find proteins for A0A4P1LYH8 (Phytophthora capsici LT1534) Explore A0A4P1LYH8  Go to UniProtKB:  A0A4P1LYH8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	C [auth A], D [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-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: 2.35 Å
• R-Value Free:  0.217 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.724	α = 80.18
b = 63.782	β = 65.27
c = 72.845	γ = 71.17

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Song, W.W., Zhang, X.G.

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Funding Organization	Location	Grant Number
	China	CARS-25-03B

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary