6IUQ

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.217
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Song, W.W., Zhang, X.G.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4P1LYH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.184
R-Value Observed: 0.186
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2018-12-12
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.