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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.217 (Depositor), 0.215 (DCC)
R-Value Work:
0.184 (Depositor), 0.187 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6IUQ

This is version 1.1 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
Modeled Residue Count: 591
Deposited Residue Count: 690
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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 (Depositor), 0.215 (DCC)
R-Value Work: 0.184 (Depositor), 0.187 (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

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View more in-depth experimental data

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
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.