7YBB

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate and factor X-derived peptide (39mer-4Ser)

• PDB DOI: https://doi.org/10.2210/pdb7YBB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-06-29 Released: 2023-07-05 
• Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate and factor X-derived peptide (39mer-4Ser)

Nakashima, Y., Brewitz, L., Schofield, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 53.81 kDa 
• Atom Count: 4,005 
• Modelled Residue Count: 447 
• Deposited Residue Count: 468 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl/asparaginyl beta-hydroxylase	A	429	Homo sapiens	Mutation(s): 0  Gene Names: ASPH EC: 1.14.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q12797 (Homo sapiens) Explore Q12797  Go to UniProtKB:  Q12797
PHAROS:  Q12797 GTEx:  ENSG00000198363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	39	synthetic construct	Mutation(s): 4  Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IO9 (Subject of Investigation/LOI)	D [auth A]	(2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid C5 H6 O6 WXSKVKPSMAHCSG-UWTATZPHSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.457	α = 90
b = 123.608	β = 90
c = 50.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description