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- PDB-7e6j: Aspartyl/Asparaginyl beta-hydroxylase (AspH) H725A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7e6j
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) H725A in complex with Factor X peptide fragment (39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Peptide from Factor X light chain
KeywordsOXIDOREDUCTASE / Aspartyl/asparaginyl beta-hydroxylase / Dioxygenase
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis / coagulation factor Xa / pattern specification process / positive regulation of intracellular protein transport / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / activation of cysteine-type endopeptidase activity / face morphogenesis / Extrinsic Pathway of Fibrin Clot Formation / structural constituent of muscle / positive regulation of calcium ion transport into cytosol / response to ATP / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / positive regulation of TOR signaling / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / Intrinsic Pathway of Fibrin Clot Formation / muscle contraction / calcium ion transmembrane transport / phospholipid binding / regulation of protein stability / Stimuli-sensing channels / Golgi lumen / blood coagulation / cell population proliferation / transmembrane transporter binding / electron transfer activity / 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 / structural molecule activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / 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 / Coagulation Factor Xa inhibitory site ...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-type aspartate/asparagine hydroxylation site / EGF-like domain / 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. / TPR repeat profile. / Epidermal growth factor-like domain. / Tetratricopeptide repeats / Tetratricopeptide repeat / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Tetratricopeptide-like helical domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
PROPANOIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakashima, Y. / Brasnett, A. / Brewitz, L. / Schofield, C.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Human Oxygenase Variants Employing a Single Protein Fe II Ligand Are Catalytically Active.
Authors: Brasnett, A. / Pfeffer, I. / Brewitz, L. / Chowdhury, R. / Nakashima, Y. / Tumber, A. / McDonough, M.A. / Schofield, C.J.
History
DepositionFeb 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Peptide from Factor X light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8796
Polymers53,5292
Non-polymers3504
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-6 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.237, 86.841, 123.542
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: 49338.270 Da / Num. of mol.: 1 / Mutation: H725A
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 Peptide from Factor X light chain / / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM PCTP, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.9→46.54 Å / Num. obs: 82246 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.792 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2159 / CC1/2: 0.699 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTC

5jtc


Resolution: 1.9→46.54 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 3800 4.62 %
Rwork0.1702 78446 -
obs0.1722 82246 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 17 364 3947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243710
X-RAY DIFFRACTIONf_angle_d0.57085012
X-RAY DIFFRACTIONf_chiral_restr0.0387526
X-RAY DIFFRACTIONf_plane_restr0.0032655
X-RAY DIFFRACTIONf_dihedral_angle_d22.07121396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.43091380.35152887X-RAY DIFFRACTION98.69
1.92-1.950.30811410.32432893X-RAY DIFFRACTION99.61
1.95-1.980.3021400.29662877X-RAY DIFFRACTION99.87
1.98-20.29891400.27352904X-RAY DIFFRACTION99.93
2-2.030.26191450.25742907X-RAY DIFFRACTION99.84
2.03-2.070.27021400.25732928X-RAY DIFFRACTION99.93
2.07-2.10.25961400.23312903X-RAY DIFFRACTION99.97
2.1-2.140.24441420.22352887X-RAY DIFFRACTION100
2.14-2.170.23111430.19632947X-RAY DIFFRACTION100
2.17-2.220.24091350.20822874X-RAY DIFFRACTION100
2.22-2.260.24631390.19672914X-RAY DIFFRACTION99.97
2.26-2.310.22471420.18992900X-RAY DIFFRACTION99.97
2.31-2.360.23681370.18022885X-RAY DIFFRACTION100
2.36-2.420.23451400.17752941X-RAY DIFFRACTION100
2.42-2.490.21761390.16932910X-RAY DIFFRACTION99.97
2.49-2.560.22281390.17152922X-RAY DIFFRACTION100
2.56-2.650.21371380.17272915X-RAY DIFFRACTION100
2.65-2.740.23321430.16522895X-RAY DIFFRACTION100
2.74-2.850.22261430.16942890X-RAY DIFFRACTION99.93
2.85-2.980.2031390.16552900X-RAY DIFFRACTION99.97
2.98-3.140.18361480.16762937X-RAY DIFFRACTION100
3.14-3.330.24431420.16222917X-RAY DIFFRACTION100
3.33-3.590.17261420.14332913X-RAY DIFFRACTION100
3.59-3.950.16061370.13082871X-RAY DIFFRACTION100
3.95-4.520.17921390.11542925X-RAY DIFFRACTION100
4.52-5.690.16051450.13082888X-RAY DIFFRACTION100
5.7-46.540.23831440.1772916X-RAY DIFFRACTION99.97
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)
15.63038637985-1.497794827890.6101959697424.09426503577-0.596631690224.275591549220.3108414737250.5733944552480.440655143788-0.530092294162-0.318712107553-0.603677025786-0.009168134460920.281163480077-0.01292052303670.46112451070.102431188640.122702512310.3753492049170.0239871752790.386178731796-6.77169332948-5.24405894861-6.42140766778
20.6908286686040.294087320314-1.467471252392.15951950054-2.650359638573.564068693290.196641288438-0.03522382512340.02732091461150.00362097282640.01931720848940.07254550821960.0449390789063-0.19648430748-0.1986558984280.352578481498-0.106962485403-0.06575163424160.367306905784-0.004678578616460.284667608829-18.8599617516-16.405411750717.10371163
31.741272616320.1655237889270.8898041422130.8700801501010.03925726162531.89816453956-0.03618017649520.282604224374-0.0758922920308-0.1505796088310.0642228200992-0.005218393522460.118138573280.1660723451-0.03202852892690.246865920460.004239757132060.006313695619950.277944483531-0.003085515886380.267838082231-3.90195903704-25.708574884745.559698279
46.32939796069-0.5226226829533.995235690493.066744941470.6724358842858.19758139613-0.3577184658110.3576134742140.59677711011-0.410703142163-0.08512805271130.11079825542-0.7446910661270.1162956781350.3793929743850.359011361393-0.037380286268-0.05234251684380.4692766305530.01639787001780.340202914319-11.3152165761-18.802884470332.6672522365
54.313568687110.4911116915265.136888729848.71329905975-1.012607402682.00015400045-0.1715382688221.127754373570.381942584789-0.0534402681290.04353472188190.0351591937121-0.000479265172505-1.046234875120.1096888570320.536701707372-0.0854744884828-0.1310276678390.8260762968210.1239610174270.488073818194-1.96666458394-9.3671746613121.4713243366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 374 )
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 538 )
3X-RAY DIFFRACTION3chain 'A' and (resid 539 through 758 )
4X-RAY DIFFRACTION4chain 'B' and (resid 99 through 113 )
5X-RAY DIFFRACTION5chain 'B' and (resid 114 through 116 )

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