[English] 日本語
Yorodumi
- PDB-9ho1: Room temperature structure of Aspartyl/Asparaginyl beta-hydroxyla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ho1
TitleRoom temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, and hydroxylated Factor X derived peptide fragment, 1.5 s O2 exposure
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Factor X light chain
KeywordsOXIDOREDUCTASE / AspH / Aspartyl/Asparaginyl beta-hydroxylase / O2 exposure / product complex
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / : / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / positive regulation of intracellular protein transport ...peptide-aspartate beta-dioxygenase / : / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / positive regulation of intracellular protein transport / cortical endoplasmic reticulum / coagulation factor Xa / pattern specification process / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / face morphogenesis / structural constituent of muscle / response to ATP / roof of mouth development / positive regulation of calcium ion transport into cytosol / Protein hydroxylation / positive regulation of proteolysis / positive regulation of TOR signaling / detection of calcium ion / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Intrinsic Pathway of Fibrin Clot Formation / Ion homeostasis / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / phospholipid binding / calcium ion transmembrane transport / regulation of protein stability / Golgi lumen / Stimuli-sensing channels / blood coagulation / transmembrane transporter binding / electron transfer activity / cell population proliferation / positive regulation of cell migration / endoplasmic reticulum lumen / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / TPR repeat region circular profile. / Epidermal growth factor-like domain. / TPR repeat profile. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Tetratricopeptide-like helical domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / SUCCINIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
Authorsde Munnik, M. / Rabe, P. / Brewitz, L. / Brasnett, A. / Zhou, T. / Schofield, C.J. / Kern, J.F.
Funding support United Kingdom, United States, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM149528-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
CitationJournal: To Be Published
Title: Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, and hydroxylated Factor X derived peptide fragment, 1.5 s O2 exposure
Authors: de Munnik, M. / Rabe, P. / Brewitz, L. / Brasnett, A. / Zhou, T. / Schofield, C.J. / Kern, J.F.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Factor X light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9325
Polymers53,6122
Non-polymers3203
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20 kcal/mol
Surface area19010 Å2
Unit cell
Length a, b, c (Å)50.850, 90.545, 124.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Aspartyl/asparaginyl beta-hydroxylase / Aspartate beta-hydroxylase / ASP beta-hydroxylase / Peptide-aspartate beta-dioxygenase


Mass: 49405.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Factor X light chain


Mass: 4206.383 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00742

-
Non-polymers , 4 types, 172 molecules

#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Description: Needle morphology, average distribution ~3 um x 3 um x 80 um
Crystal growTemperature: 278 K / Method: batch mode / pH: 7.5
Details: 16% PEG3350, 0.1M Bis Tris propane pH 7.5, 0.1 M KSCN

-
Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.266025 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jun 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.266025 Å / Relative weight: 1
ReflectionResolution: 1.85→23.96 Å / Num. obs: 49970 / % possible obs: 99.91 % / Redundancy: 43.92 % / Biso Wilson estimate: 33.87 Å2 / CC1/2: 0.977 / R split: 0.156 / Net I/σ(I): 5.01
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 0.794 / Num. unique obs: 2485 / CC1/2: 0.373 / R split: 0.868 / % possible all: 99.68
Serial crystallography measurementPulse photon energy: 1.8 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: ADE tape drive / Method: injection
Serial crystallography sample delivery injectionFlow rate: 6 µL/min

-
Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→23.96 Å / SU ML: 0.2853 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 2000 4.01 %
Rwork0.1975 47886 -
obs0.1984 49886 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.25 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 19 169 3647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583585
X-RAY DIFFRACTIONf_angle_d0.70074862
X-RAY DIFFRACTIONf_chiral_restr0.0474518
X-RAY DIFFRACTIONf_plane_restr0.0063641
X-RAY DIFFRACTIONf_dihedral_angle_d14.44261315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.41131400.36333358X-RAY DIFFRACTION99.21
1.9-1.950.34761400.33953346X-RAY DIFFRACTION99.89
1.95-20.35831410.3123383X-RAY DIFFRACTION100
2-2.070.31521420.27553375X-RAY DIFFRACTION100
2.07-2.140.31211410.25823390X-RAY DIFFRACTION100
2.14-2.230.30291410.25123386X-RAY DIFFRACTION100
2.23-2.330.27141420.25043395X-RAY DIFFRACTION100
2.33-2.450.28471420.23043397X-RAY DIFFRACTION100
2.45-2.610.26731420.2273409X-RAY DIFFRACTION99.97
2.61-2.810.27711440.22793434X-RAY DIFFRACTION99.97
2.81-3.090.23521420.2173412X-RAY DIFFRACTION99.94
3.09-3.540.23431450.18913461X-RAY DIFFRACTION100
3.54-4.450.14571450.14573487X-RAY DIFFRACTION99.86
4.45-23.960.15111530.14773653X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 9.800882563915 Å / Origin y: 20.279023473484 Å / Origin z: 30.772225871839 Å
111213212223313233
T0.31113052986376 Å2-0.028832419824873 Å20.026581152929471 Å2-0.3839191383924 Å20.022867072298252 Å2--0.35202256293826 Å2
L0.16723684363867 °2-0.51642158397778 °2-0.297267832841 °2-0.75646154730369 °21.010432298708 °2--2.5220504359795 °2
S0.11327909826489 Å °0.17744068017685 Å °0.025857013328368 Å °-0.21352898737878 Å °-0.029979673456609 Å °-0.079556381921338 Å °-0.21069172698976 Å °-0.028821106520953 Å °-0.079469381295128 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more