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

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Basic information

Entry
Database: PDB / ID: 7ybc
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with (S)-4-hydroxy-4-methyl-2-oxoglutarate 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 / positive regulation of intracellular protein transport / 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 / positive regulation of calcium ion transport into cytosol / positive regulation of ryanodine-sensitive calcium-release channel activity / roof of mouth development / Protein hydroxylation / positive regulation of proteolysis / regulation of ryanodine-sensitive calcium-release channel activity / 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 / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / calcium ion homeostasis / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Intrinsic Pathway of Fibrin Clot Formation / muscle contraction / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / regulation of protein stability / calcium ion transmembrane transport / phospholipid binding / Stimuli-sensing channels / Golgi lumen / blood coagulation / transmembrane transporter binding / electron transfer activity / cell population proliferation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / negative regulation of cell population proliferation / 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 / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Tetratricopeptide repeat domain / 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 Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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 / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-IOW / : / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 (S)-4-hydroxy-4-methyl-2-oxoglutarate 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)53,9195
Polymers53,5962
Non-polymers3233
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-15 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.372, 87.049, 124.396
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

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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 / 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

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Non-polymers , 4 types, 313 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IOW / (2~{S})-2-methyl-2-oxidanyl-4-oxidanylidene-pentanedioic acid


Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 20 % w/v Polyethylene glycol 3,350, 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: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.84→71.32 Å / Num. obs: 48417 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 27.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.081 / Rrim(I) all: 0.29 / Net I/σ(I): 8.5
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 13.2 % / Rmerge(I) obs: 4.176 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2389 / CC1/2: 0.399 / Rpim(I) all: 1.195 / Rrim(I) all: 4.345 / % possible all: 100

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Processing

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

5jtc


Resolution: 1.84→43.6 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1987 2324 4.81 %
Rwork0.1776 46033 -
obs0.1786 48357 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.06 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 0 310 3891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493713
X-RAY DIFFRACTIONf_angle_d0.78595026
X-RAY DIFFRACTIONf_chiral_restr0.0445528
X-RAY DIFFRACTIONf_plane_restr0.0045659
X-RAY DIFFRACTIONf_dihedral_angle_d20.25691394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.33931530.32272626X-RAY DIFFRACTION98.69
1.88-1.920.30411480.29642630X-RAY DIFFRACTION99.46
1.92-1.960.29871640.2662635X-RAY DIFFRACTION99.96
1.96-2.010.29191190.24232703X-RAY DIFFRACTION100
2.01-2.060.27321270.22282662X-RAY DIFFRACTION99.96
2.06-2.130.22581350.21252691X-RAY DIFFRACTION100
2.13-2.190.19511260.18072715X-RAY DIFFRACTION99.96
2.19-2.270.24061230.18152676X-RAY DIFFRACTION100
2.27-2.360.20221110.17462704X-RAY DIFFRACTION100
2.36-2.470.24451430.17442691X-RAY DIFFRACTION100
2.47-2.60.19231350.16762697X-RAY DIFFRACTION100
2.6-2.760.23381480.17482704X-RAY DIFFRACTION100
2.76-2.980.20761460.17162718X-RAY DIFFRACTION99.97
2.98-3.280.20521400.17342718X-RAY DIFFRACTION100
3.28-3.750.14861230.15482757X-RAY DIFFRACTION100
3.75-4.730.13931460.13362779X-RAY DIFFRACTION99.97
4.73-43.60.19451370.18542927X-RAY DIFFRACTION99.77
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)
10.467860874496-0.152993387091-0.4791436950941.3125873603-1.172715755351.398088539230.189802593346-0.01650582884340.0922138591403-0.0788637883492-0.03403766763070.001692711252770.0654387307526-0.1630414524270.00220155361570.308893083668-0.0764576028283-0.02655816536780.280234886931-0.007204564508680.250694567887-16.4226408393-13.893830682312.1514564595
21.38219021430.3278223579330.859924265990.7544563209480.1601625789321.15795165887-0.03759055608340.253369726883-0.0179665436055-0.1061147521220.0887482114642-0.01608912604790.0377322816210.1697564966160.0004014129243730.19962764828-0.003452442121010.004418897912940.216818388617-0.001676348928720.215455282371-3.98926691954-25.608834248445.766678427
30.00715296941525-0.01192878734270.0062629234680.0335300394317-0.01376614678910.00467797769970.1728626371160.07659391415810.076908454693-0.0627272752959-0.09810958872030.0366964002098-0.0783827392527-0.0508102426838-0.0002070979413660.3653002163710.0221591109894-0.03831746671540.654604834444-0.01656495207120.346592778434-10.4741373048-18.789948538238.5762695587
40.005636282310970.004828351315645.23187295896E-50.0102635713302-0.01177238163230.01217957101960.07492708577020.03591934173060.130844161549-0.1123451113-0.01286397385460.0488501253247-0.0982559789967-0.190612239431.44664699763E-50.37565296104-0.0678535384357-0.03700085816380.4770396393410.006959386656090.313395224012-14.6273932573-21.766173210231.5899213895
50.02031437461020.012417334188-0.009885546387480.0239749976339-0.006094302369570.0134121402995-0.34223507580.0247404184255-0.0196447701182-0.168819694622-0.2623774705390.143342357251-0.08498475119040.0360372142118-0.0002284994685880.499389367402-0.128704880817-0.05557002571250.6273937102490.07582681453510.312311034217-8.64669770845-15.847854250628.1199394951
60.114470305323-0.0116087151215-0.2478803601170.002329604659880.043038745590.6953551742990.05250566895470.001740644920880.02527611145850.0738319855691-0.0204150184334-0.1215344997940.02310081115980.0465153678545-8.39309183132E-60.46542388653-0.187351937795-0.1311629773520.7729270844220.1868126174760.521274879363-1.62750604403-9.7975559176720.1105423758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 538 )
2X-RAY DIFFRACTION2chain 'A' and (resid 539 through 758 )
3X-RAY DIFFRACTION3chain 'B' and (resid 99 through 103 )
4X-RAY DIFFRACTION4chain 'B' and (resid 104 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 116 )

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