7E08 | pdb_00007e08

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

PDB DOI: https://doi.org/10.2210/pdb7E08/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: 1.84 Å
R-Value Free:
0.231 (Depositor), 0.241 (DCC)
R-Value Work:
0.196 (Depositor), 0.208 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Trans-3/4-proline-hydroxylase H11 4-Hydroxyl-proline

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

To be published.

Macromolecule Content

Total Structure Weight: 30 kDa
Atom Count: 2,251
Modeled Residue Count: 263
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S5TUM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HYP (Subject of Investigation/LOI) Query on HYP 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]	4-HYDROXYPROLINE C₅ H₉ N O₃ PMMYEEVYMWASQN-DMTCNVIQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.231 (Depositor), 0.241 (DCC)
R-Value Work: 0.196 (Depositor), 0.208 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.289	α = 90
b = 75.289	β = 90
c = 144.544	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

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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 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.