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- PDB-9hnz: Room temperature structure of Aspartyl/Asparaginyl beta-hydroxyla... -

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Basic information

Entry
Database: PDB / ID: 9hnz
TitleRoom temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and hydroxylated Factor X derived peptide fragment, 2 h 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
: / SUCCINIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsde Munnik, M. / Rabe, P. / Brasnett, A. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
Wellcome Trust227298/Z/23/Z United Kingdom
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, 2 h O2 exposure
Authors: de Munnik, M. / Rabe, P. / Brasnett, A. / Brewitz, L. / Schofield, C.J.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,7864
Polymers53,6122
Non-polymers1742
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-23 kcal/mol
Surface area18930 Å2
Unit cell
Length a, b, c (Å)50.880, 90.404, 124.625
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

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Components

#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
#3: Chemical ChemComp-SIN / SUCCINIC ACID


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


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


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.6 %
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, 0.1 M bis tris propane pH 7.5, 0.1 M KSCN

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.4→73.18 Å / Num. obs: 23199 / % possible obs: 99.98 % / Redundancy: 54.81 % / Biso Wilson estimate: 55.44 Å2 / CC1/2: 0.968 / R split: 0.203 / Net I/σ(I): 2.826
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 33.52 % / Mean I/σ(I) obs: 0.427 / Num. unique obs: 1147 / CC1/2: 0.135 / R split: 1.117 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
DIALSdials.stills_processdata reduction
cctbx.xfel.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→73.18 Å / SU ML: 0.4423 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 2000 8.79 %
Rwork0.2016 20750 -
obs0.2048 22750 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→73.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 9 50 3508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173548
X-RAY DIFFRACTIONf_angle_d0.42664814
X-RAY DIFFRACTIONf_chiral_restr0.0375516
X-RAY DIFFRACTIONf_plane_restr0.0032631
X-RAY DIFFRACTIONf_dihedral_angle_d12.36441289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.39121260.37091298X-RAY DIFFRACTION87.58
2.46-2.530.42141330.36171397X-RAY DIFFRACTION93.46
2.53-2.60.35551370.35421417X-RAY DIFFRACTION95.63
2.6-2.680.42211400.34691450X-RAY DIFFRACTION97.61
2.68-2.780.38951420.34841467X-RAY DIFFRACTION99.2
2.78-2.890.35481430.31261488X-RAY DIFFRACTION99.21
2.89-3.020.28411430.27531490X-RAY DIFFRACTION99.76
3.02-3.180.3011470.25831516X-RAY DIFFRACTION99.88
3.18-3.380.25941420.23071484X-RAY DIFFRACTION99.88
3.38-3.640.22221460.19711502X-RAY DIFFRACTION100
3.64-4.010.24521450.15371514X-RAY DIFFRACTION100
4.01-4.590.18261490.13791534X-RAY DIFFRACTION99.94
4.59-5.780.19291490.15571556X-RAY DIFFRACTION100
5.78-73.180.16291580.15241637X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4456144089380.3679074408060.7194160771573.899324587643.176070755084.837995049540.2553785816260.0878388113812-0.0101438832443-0.2098384384370.0919462876634-0.186526035064-0.2522064797730.324473350808-0.3139688439170.41819477024-0.02354558074080.08459328565920.6364915478020.05668075348870.45905063158516.074093460715.439870061913.4663693905
22.696491636630.434503239129-1.646345150862.01653588215-0.2958612061054.1624478276-0.01584917982080.3511846808580.118797135868-0.2131569957370.08966604578470.00352472374637-0.138539766729-0.359445204356-0.06694985261030.2735216470690.0184394734703-0.009377545142140.4926921103750.01314124774410.324392351713.5560358011125.305337422847.0696813521
35.23868692469-1.68861111516-3.479658423347.350017079695.56051864056.875668188870.03058821080980.59273190423-0.1468105651840.0167160715180.642446376749-0.455042299165-0.002962261080261.00253727799-0.6811457964260.5388062258120.02955182238720.03447799230360.64651224858-0.007832853110040.53162624156612.345401475520.973073226134.1981675796
41.24110555-1.44385586325-1.481703755625.622391454814.944620102564.39996981756-0.5999331368721.08132527207-1.3792344904-0.559631790719-0.1741572147230.587139748782-0.224571363346-0.4042451198270.8559564975840.834741597752-0.1489885073760.1337768582120.852962646458-0.2346243139440.7575200751945.709243219812.2110414726.1957270601
56.687404850136.20122851636-3.215579577047.78876290241-6.491266479917.58840477425-1.33758534252.5468206954-1.472815820291.014700142240.688953116005-0.1402130749830.432734354276-1.994119001010.660009372591.50291206625-0.2635660384-0.7768990466281.01333215990.04153668727661.94696638685-0.3836284498359.4048650285618.399395297
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 330 through 553 )AA330 - 5531 - 224
22chain 'A' and (resid 554 through 758 )AA554 - 758225 - 429
33chain 'B' and (resid 100 through 110 )BC100 - 1101 - 11
44chain 'B' and (resid 111 through 115 )BC111 - 11512 - 16
55chain 'B' and (resid 116 through 116 )BC11617

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