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- PDB-7yb9: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -

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Basic information

Entry
Database: PDB / ID: 7yb9
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with L-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor X
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 / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum ...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 / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum / 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 / response to ATP / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of TOR signaling / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / calcium ion homeostasis / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / Intrinsic Pathway of Fibrin Clot Formation / cellular response to calcium ion / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / phospholipid binding / Golgi lumen / blood coagulation / transmembrane transporter binding / cell population proliferation / electron transfer activity / positive regulation of cell migration / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / 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 ...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. / TPR repeat profile. / Epidermal growth factor-like domain. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Tetratricopeptide-like helical domain superfamily / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / (2S)-2-HYDROXYPENTANEDIOIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with L-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser)
Authors: Nakashima, Y. / Brewitz, L. / Schofield, C.J.
History
DepositionJun 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9284
Polymers53,7252
Non-polymers2032
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-15 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.672, 91.895, 123.073
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: 49534.516 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) / Strain (production host): BL21(DE3)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 4190.384 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: F10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-S2G / (2S)-2-HYDROXYPENTANEDIOIC ACID


Mass: 148.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium chloride, 20 % w/v Polyethylene glycol 6,000, 0.1 M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.54→91.9 Å / Num. obs: 83496 / % possible obs: 99.2 % / Redundancy: 13.2 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Net I/σ(I): 12.1
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 11.8 % / Rmerge(I) obs: 3.633 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3963 / CC1/2: 0.356 / Rpim(I) all: 1.09 / Rrim(I) all: 3.797 / % possible all: 95.5

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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: 1.54→73.63 Å / SU ML: 0.2137 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 1806 2.39 %
Rwork0.1849 73891 -
obs0.1857 75697 90.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.47 Å2
Refinement stepCycle: LAST / Resolution: 1.54→73.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 0 408 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113711
X-RAY DIFFRACTIONf_angle_d1.1315025
X-RAY DIFFRACTIONf_chiral_restr0.057528
X-RAY DIFFRACTIONf_plane_restr0.0076658
X-RAY DIFFRACTIONf_dihedral_angle_d19.29571396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.3054130.4482572X-RAY DIFFRACTION9.21
1.59-1.630.39721030.40124509X-RAY DIFFRACTION72.6
1.63-1.680.3511490.36016106X-RAY DIFFRACTION98.46
1.68-1.740.33191510.31716136X-RAY DIFFRACTION98.95
1.74-1.810.33571520.28296153X-RAY DIFFRACTION99.17
1.81-1.90.26671510.25936202X-RAY DIFFRACTION99.41
1.9-20.26411530.226177X-RAY DIFFRACTION99.12
2-2.120.21241520.19346217X-RAY DIFFRACTION99.66
2.12-2.290.23211540.18926249X-RAY DIFFRACTION99.6
2.29-2.520.22991540.1856274X-RAY DIFFRACTION99.75
2.52-2.880.19241540.19096312X-RAY DIFFRACTION99.88
2.88-3.630.23141580.17356354X-RAY DIFFRACTION99.98
3.63-73.630.17191620.14996630X-RAY DIFFRACTION99.82
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)
10.840150929538-0.247525672316-0.1129616125510.8153484292840.8489948816340.876838592680.2666911411180.0785669328837-0.0870020599555-0.050554556974-0.2168241885320.174494744183-0.104902277631-0.1129580114412.85168821129E-50.3781687500370.0204541059262-0.002436430527640.254125077857-0.0399859703540.37491720968860.442601765839.352946911356.9331808733
21.62920599244-0.2619635213721.780901726230.3863281545010.01120282275813.092598095180.0611123979004-0.261236122186-0.1082585378570.06375034000080.132240202263-0.05692935807590.288566152425-0.4152068451590.006069064661030.246890660891-0.0285967716601-0.01053001351620.2419894940130.0143641064770.26830727288957.750645859719.315490896521.460836234
3-0.00508986764233-0.001719854671640.005042131797160.001424087415970.01289448045470.01422732097430.04909083697820.0784733764377-0.0220607953965-0.1089395156640.080360945144-0.07412145903020.08069025888060.088079045509-0.0001038073794830.3187686603790.0175552407849-0.05294547214710.374732193271-0.005193504851640.33722892548561.554684464325.138968074527.31782929
40.0193615354907-0.024104018855-0.01787330097070.06180194152370.02396129538610.0139068410922-0.0734169992684-0.02335080920180.1528750680620.0654569911193-0.0217618070468-0.08144185966860.00786105494786-0.0911998849104-0.0002624860839220.5089535791770.116253181252-0.03744068881770.5584010618-0.09710276843620.29494229311557.252621456629.656695981633.6862118439
50.01834218957490.0090967362486-0.05367070460920.00484044063858-0.02978139990550.179009185874-0.01201255154960.134944309320.0895536428707-0.05357913957930.0169254850871-0.006923706606710.001465239564540.0787840168368-0.002084179617230.7381246802520.0956689835620.07249166658270.735367553238-0.2653961214940.64478304034349.587497624535.20988543142.5429106015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 329 through 467 )
2X-RAY DIFFRACTION2chain 'A' and (resid 468 through 758 )
3X-RAY DIFFRACTION3chain 'B' and (resid 99 through 108 )
4X-RAY DIFFRACTION4chain 'B' and (resid 109 through 113 )
5X-RAY DIFFRACTION5chain 'B' and (resid 114 through 116 )

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