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

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Basic information

Entry
Database: PDB / ID: 7ybb
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-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 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 / Protein hydroxylation / roof of mouth development / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / detection of calcium ion / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Removal of aminoterminal propeptides from gamma-carboxylated proteins / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / Intrinsic Pathway of Fibrin Clot Formation / calcium channel complex / sarcoplasmic reticulum membrane / muscle contraction / cellular response to calcium ion / phospholipid binding / regulation of protein stability / calcium ion transmembrane transport / Stimuli-sensing channels / Golgi lumen / 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 / 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-IO9 / : / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 D-4-hydroxy-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 23, 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

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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)53,8134
Polymers53,5962
Non-polymers2172
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-15 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.457, 123.608, 50.183
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 / 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
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-IO9 / (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid


Mass: 162.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02 M Sodium/potassium phosphate, 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: 0.96857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96857 Å / Relative weight: 1
ReflectionResolution: 1.68→71.39 Å / Num. obs: 41711 / % possible obs: 94.7 % / Redundancy: 13 % / Biso Wilson estimate: 16.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.072 / Rrim(I) all: 0.256 / Net I/σ(I): 7.9
Reflection shellResolution: 1.68→1.83 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.978 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2087 / CC1/2: 0.594 / Rpim(I) all: 0.559 / Rrim(I) all: 2.056 / % possible all: 69.5

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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: 1.68→46.5 Å / SU ML: 0.1705 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 2000 4.8 %
Rwork0.1945 39686 -
obs0.1957 41686 66.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.01 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 0 414 3996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01343673
X-RAY DIFFRACTIONf_angle_d1.27094962
X-RAY DIFFRACTIONf_chiral_restr0.0644522
X-RAY DIFFRACTIONf_plane_restr0.0091648
X-RAY DIFFRACTIONf_dihedral_angle_d20.81781379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.730.336980.33158X-RAY DIFFRACTION3.83
1.73-1.770.3678310.3291597X-RAY DIFFRACTION14.36
1.77-1.830.3115510.28621022X-RAY DIFFRACTION24.45
1.83-1.880.3059750.26821512X-RAY DIFFRACTION36.27
1.88-1.950.32091080.28252126X-RAY DIFFRACTION50.57
1.95-2.030.26341280.23382533X-RAY DIFFRACTION60.41
2.03-2.120.24661540.2343047X-RAY DIFFRACTION72.31
2.12-2.230.24041710.2213413X-RAY DIFFRACTION81.27
2.23-2.370.22971900.22983777X-RAY DIFFRACTION88.91
2.37-2.560.25222090.21444128X-RAY DIFFRACTION97.77
2.56-2.810.21672150.21144270X-RAY DIFFRACTION100
2.81-3.220.23962150.19514265X-RAY DIFFRACTION100
3.22-4.060.17272170.15694323X-RAY DIFFRACTION100
4.06-46.50.18982280.15754515X-RAY DIFFRACTION100

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