7E09

Trans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline

PDB DOI: https://doi.org/10.2210/pdb7E09/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium esnapd13
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-27 Released: 2022-02-02
Deposition Author(s): Gong, W.G., Yang, L.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.226
R-Value Work: 0.192
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Trans-3/4-proline-hydroxylase H11 with AKG and L-proline

Gong, W.G., Yang, L.Y.

To be published.

Macromolecule Content

Total Structure Weight: 30 kDa
Atom Count: 2,103
Modelled Residue Count: 262
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytanoyl-CoA dioxygenase	A	266	uncultured bacterium esnapd13	Mutation(s): 0
UniProt
Find proteins for S5TUM1 (uncultured bacterium esnapd13) Explore S5TUM1 Go to UniProtKB: S5TUM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S5TUM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HY3 (Subject of Investigation/LOI) Query on HY3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-HYDROXYPROLINE C₅ H₉ N O₃ BJBUEDPLEOHJGE-IMJSIDKUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.226
R-Value Work: 0.192
R-Value Observed: 0.193
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.39	α = 90
b = 75.39	β = 90
c = 143.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2022-02-02
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2023-11-29
Changes: Refinement description

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.