7E00

Trans-proline-hydroxylase H11 with Succinic and L-proline in the fourth reaction state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytanoyl-CoA dioxygenase
A, B
268uncultured bacterium esnapd13Mutation(s): 0 
UniProt
Find proteins for S5TUM1 (uncultured bacterium esnapd13)
Explore S5TUM1 
Go to UniProtKB:  S5TUM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5TUM1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
E [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
SIN (Subject of Investigation/LOI)
Query on SIN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PRO (Subject of Investigation/LOI)
Query on PRO

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
O (Subject of Investigation/LOI)
Query on O

Download Ideal Coordinates CCD File 
H [auth B]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.367α = 90
b = 106.367β = 90
c = 143.924γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
  • Version 1.2: 2024-04-17
    Changes: Experimental preparation