8RE8 | pdb_00008re8

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment

• PDB DOI: https://doi.org/10.2210/pdb8RE8/pdb

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


• Deposited: 2023-12-10 Released: 2024-12-18 
• Deposition Author(s): Brasnett, A., Hou, C., Rabe, P., Brewitz, L., Schofield, C.J.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.208 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment

Brasnett, A., Hou, C., Rabe, P., 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: 56.14 kDa 
• Atom Count: 3,938 
• Modeled Residue Count: 447 
• Deposited Residue Count: 483 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl/asparaginyl beta-hydroxylase	A	444	Homo sapiens	Mutation(s): 1  Gene Names: ASPH, BAH 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  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q1Z (Subject of Investigation/LOI)	C [auth A]	(3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid C6 H8 O5 BJQIUPTURRAODO-GSVOUGTGSA-N
PEG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	I [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.208 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.604	α = 90
b = 85.998	β = 90
c = 123.963	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Brasnett, A., Hou, C., Rabe, P., Brewitz, L., Schofield, C.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106244/Z/14/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1
Wellcome Trust	United Kingdom	227298/Z/23/Z

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release