7DT0

Proline hydroxylase H11-N101I mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytanoyl-CoA dioxygenase
A, B, C, D, E
A, B, C, D, E, F, G, H
266uncultured bacterium esnapd13Mutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
PRO (Subject of Investigation/LOI)
Query on PRO

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
K [auth A]
M [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
K [auth A],
M [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
J [auth A]
N [auth B]
P [auth C]
BA [auth G],
EA [auth H],
J [auth A],
N [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.91α = 90
b = 138.64β = 90
c = 152.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2022-01-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description