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- PDB-9fw0: Room temperature structure of Aspartyl/Asparaginyl beta-hydroxyla... -

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Entry
Database: PDB / ID: 9fw0
TitleRoom temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor X
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 / : / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrasnett, A. / de Munnik, M. / Brewitz, L. / Rabe, P. / 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 Factor X derived peptide fragment
Authors: Brasnett, A. / de Munnik, M. / Brewitz, L. / Rabe, P. / Schofield, C.J. / Kern, J.F.
History
DepositionJun 28, 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

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Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6684
Polymers53,4672
Non-polymers2022
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-22 kcal/mol
Surface area19130 Å2
Unit cell
Length a, b, c (Å)50.796, 88.160, 125.161
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: 49276.156 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 Coagulation factor X


Mass: 4190.384 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Description: needle morphology, avergae distibution ~ 3 um x 3 um x 80 um
Crystal growTemperature: 278 K / Method: batch mode / pH: 7.5
Details: 16% PEG 3350, 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: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.50844 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Sep 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.50844 Å / Relative weight: 1
ReflectionResolution: 1.95→26.64 Å / Num. obs: 41728 / % possible obs: 99.86 % / Redundancy: 40.35 % / Biso Wilson estimate: 36.01 Å2 / CC1/2: 0.98 / R split: 0.152 / Net I/σ(I): 3.342
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 10.96 % / Mean I/σ(I) obs: 0.412 / Num. unique obs: 1999 / CC1/2: 0.165 / R split: 1.094 / % possible all: 98.86
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 injectionDescription: ADE tape drive / Flow rate: 7 µL/min

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→26.64 Å / SU ML: 0.3029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2066 2000 4.81 %
Rwork0.1771 39564 -
obs0.1785 41564 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.95 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 11 146 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693620
X-RAY DIFFRACTIONf_angle_d0.85934904
X-RAY DIFFRACTIONf_chiral_restr0.0503520
X-RAY DIFFRACTIONf_plane_restr0.0074643
X-RAY DIFFRACTIONf_dihedral_angle_d13.82341334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.41131330.38892612X-RAY DIFFRACTION94.46
2-2.050.34521390.34712772X-RAY DIFFRACTION99.08
2.05-2.110.33431420.30672815X-RAY DIFFRACTION99.97
2.11-2.180.30711420.27142793X-RAY DIFFRACTION100
2.18-2.260.29281410.24772796X-RAY DIFFRACTION100
2.26-2.350.26731420.22322812X-RAY DIFFRACTION100
2.35-2.460.23841420.20522817X-RAY DIFFRACTION100
2.46-2.590.21731430.20332813X-RAY DIFFRACTION100
2.59-2.750.23761440.21132848X-RAY DIFFRACTION99.97
2.75-2.960.24031420.20922827X-RAY DIFFRACTION100
2.96-3.260.21231450.17632847X-RAY DIFFRACTION100
3.26-3.730.16791440.14362869X-RAY DIFFRACTION100
3.73-4.690.16551470.11772906X-RAY DIFFRACTION99.97
4.69-26.640.14981540.13813037X-RAY DIFFRACTION99.75
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)
15.36588476441-0.355227208676-2.296999593632.551970226341.103396575662.494495806210.4405235737960.264156265671-0.0951869052421-0.353766796197-0.269541851640.376209879161-0.0500971749648-0.336266529112-0.1951735000560.4140364650830.0604653288276-0.1099298831710.337509299347-0.03667570508810.4123890079496.617066582754.716367316850.0566909712487
20.39681699070.04337684020390.7178875906982.885266067912.829073324683.724327910320.1346006452140.103413430932-0.0459181408331-0.07496949532460.204394458497-0.281710708743-0.09929200152580.441050179229-0.3076528557820.341864223091-0.1350184195460.06904124643980.519584077038-0.0362955323110.34140277522422.068842267819.482229921219.9141257346
32.12022057230.33477913817-0.8528710769661.52784190403-0.1440515619562.65307807949-0.01193189943980.3271112269590.128813386921-0.1437891643710.08265622969260.0207199191255-0.109242425489-0.191963969683-0.06513576999470.2000840196140.0119482351269-0.002107596690370.248286343170.01126376007930.2298534362794.2955206374625.981687720946.1293288298
44.213487899873.36543253566-1.037530480224.239604626590.9786798319572.36097978542-0.2362294728710.517956211189-1.04141918518-0.6491996269870.235939672697-1.318047682631.055560683671.32486411439-0.03674341025620.3953344816230.1153679556360.0591119326380.50569518728-0.01739959312660.40295968107210.812802560319.314292769338.839959196
58.59864198595-6.07893457694-6.701121348215.987437720026.112461444976.338922172780.317184867186-0.07593616172340.313902613593-0.230248265520.5983763891640.429676488611-0.6839021543981.41297950528-0.9171342363250.398360722278-0.04838194602850.0969866356010.445828627147-0.006047517356590.35410026171314.711634818921.878314958931.7126001035
67.49405098585.046555298564.91934771515.824897241325.706000871595.5913264812-0.04903971248860.847895988175-0.807779874249-0.980760228385-0.5404754326770.4718889590610.512025616335-0.5316952162860.6724568070570.589069748663-0.1076290347970.0166931949130.721239043119-0.09213104420420.4832197269768.7355676067915.981894234828.7568927641
70.3419315585180.2193316573611.010397081010.1811939834230.6663765317573.770428191670.191771304827-0.2867996625040.00810236834502-0.00706655578252-0.1048344256990.1780183749240.035394879519-0.491793422052-0.09494242616610.670537794665-0.2679137283650.02691006573940.788686272741-0.2475309771610.6889426806951.42777282519.4847770388520.3617703086
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 331 through 410 )AA331 - 4101 - 80
22chain 'A' and (resid 411 through 538 )AA411 - 53881 - 208
33chain 'A' and (resid 539 through 758 )AA539 - 758209 - 428
44chain 'B' and (resid 99 through 103 )BC99 - 1031 - 5
55chain 'B' and (resid 104 through 108 )BC104 - 1086 - 10
66chain 'B' and (resid 109 through 113 )BC109 - 11311 - 15
77chain 'B' and (resid 114 through 116 )BC114 - 11616 - 18

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