7E01 | pdb_00007e01

Trans-3/4-proline-hydroxylase H11 in the sixth reaction state

• PDB DOI: https://doi.org/10.2210/pdb7E01/pdb

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


• Deposited: 2021-01-26 Released: 2022-02-02 
• Deposition Author(s): Gong, W.G., Yang, L.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

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

Gong, W.G., Yang, L.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.01 kDa 
• Atom Count: 2,288 
• Modeled Residue Count: 264 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO (Subject of Investigation/LOI)	B [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
O (Subject of Investigation/LOI)	C [auth A], D [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.367	α = 90
b = 75.367	β = 90
c = 144.753	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

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Gong, W.G., Yang, L.Y.

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

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-04-17
  Changes: Experimental preparation