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

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Basic information

Entry
Database: PDB / ID: 7bmi
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (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 / 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 / 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 / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / 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
: / 3-fluoranylpyridine-2,4-dicarboxylic acid / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: J Fluor Chem / Year: 2021
Title: Fluorinated derivatives of pyridine-2,4-dicarboxylate are potent inhibitors of human 2-oxoglutarate dependent oxygenases
Authors: Brewitz, L. / Nakashima, Y. / Tumber, A. / Salah, E. / Schofield, C.J.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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)53,8364
Polymers53,5962
Non-polymers2402
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-13 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.702, 91.274, 122.629
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, BAH / Production host: Escherichia coli BL21(DE3) (bacteria)
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: obtained synthetically / Source: (synth.) Homo sapiens (human) / 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-U4B / 3-fluoranylpyridine-2,4-dicarboxylic acid


Mass: 185.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4FNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES sodium, 200 mM ammonium chloride, 20% w/v PEG 4000, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.66→46.06 Å / Num. obs: 116324 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.9
Reflection shellResolution: 1.66→1.69 Å / Rmerge(I) obs: 4.209 / Num. unique obs: 3237 / CC1/2: 0.312

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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: 1.66→46.06 Å / SU ML: 0.2556 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 3476 2.99 %
Rwork0.189 112848 -
obs0.19 116324 91.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.41 Å2
Refinement stepCycle: LAST / Resolution: 1.66→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 0 375 3957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513723
X-RAY DIFFRACTIONf_angle_d1.09665040
X-RAY DIFFRACTIONf_chiral_restr0.0685527
X-RAY DIFFRACTIONf_plane_restr0.0085662
X-RAY DIFFRACTIONf_dihedral_angle_d21.54561400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.5945230.4672699X-RAY DIFFRACTION14.33
1.68-1.710.5002440.4491469X-RAY DIFFRACTION29.48
1.71-1.730.4297910.44152876X-RAY DIFFRACTION58.45
1.73-1.760.45731270.43764186X-RAY DIFFRACTION84.73
1.76-1.790.42991520.40844866X-RAY DIFFRACTION97.97
1.79-1.820.40371530.38134916X-RAY DIFFRACTION99.82
1.82-1.850.3311520.36934903X-RAY DIFFRACTION99.94
1.85-1.890.28381530.33534951X-RAY DIFFRACTION99.98
1.89-1.930.37811510.31794972X-RAY DIFFRACTION99.96
1.93-1.970.31271510.27834894X-RAY DIFFRACTION99.94
1.97-2.010.29941560.25214960X-RAY DIFFRACTION99.86
2.01-2.060.23581530.22744954X-RAY DIFFRACTION100
2.06-2.120.21891540.22094926X-RAY DIFFRACTION99.98
2.12-2.180.28491500.20374938X-RAY DIFFRACTION100
2.18-2.250.22581560.19994964X-RAY DIFFRACTION99.94
2.25-2.330.23041410.19744916X-RAY DIFFRACTION99.92
2.33-2.430.26081530.18954938X-RAY DIFFRACTION100
2.43-2.540.23281530.18724957X-RAY DIFFRACTION100
2.54-2.670.1871510.19044921X-RAY DIFFRACTION100
2.67-2.840.23751500.18174938X-RAY DIFFRACTION100
2.84-3.060.21781510.1814968X-RAY DIFFRACTION99.98
3.06-3.360.19091500.1734935X-RAY DIFFRACTION100
3.37-3.850.18511540.15374958X-RAY DIFFRACTION100
3.85-4.850.16991530.13334920X-RAY DIFFRACTION100
4.85-46.060.2031540.16724923X-RAY DIFFRACTION99.65
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)
12.884434078911.299356832170.6364647148792.437301864291.154187487944.183010737130.35037141817-0.7408549035170.04528319830890.328997469216-0.4140445810540.7027148906460.0488521236682-0.6216449011380.06107490850130.527122940815-0.08515017124130.06096951390950.5028930557340.01979581070420.57466992010155.765542411641.879373005868.0981473888
20.6938652023180.110985709415-0.7057304393381.312142074781.783128726323.777894450360.490857011690.40476831019-0.103190363018-0.224533157852-0.3382312610740.236269932914-0.401960510379-0.266806793619-0.07705291236760.5606717432170.124610733236-0.0459381667050.373294122766-0.04651908084610.48155742054262.716281984637.691407978151.3264173956
32.13553717438-0.3894259139672.234415596480.9956452601710.2575267394593.862611611590.0359904797892-0.421812136195-0.1457765048740.181884502810.194627659951-0.09842630002610.383589919071-0.550538238334-0.1311955529710.268686481806-0.0312280839252-0.009824023224610.3124444175790.02267228059640.28095362244157.886752112319.080596104221.1978804468
41.462776857091.139963031192.724013860690.9066377089261.945773011676.67818744092-0.0915665699484-0.1123625840210.04996540012850.359337555429-0.0394400871903-0.249254310676-0.1834523573-0.115808642942-0.1507184822350.3794167671760.0604974957326-0.07166066480440.495544017792-0.04410668103150.39176415213161.410601472824.50485360726.4855785953
50.1342300178940.1053747047870.5288855396130.1440105583670.5668006290092.465226847140.022910424077-0.3361076788080.561333810760.153409071509-0.1036965003120.0145412421354-0.399392679228-0.846761059387-0.1115567418530.6208648700950.153053063183-0.05183640604760.791383004761-0.1524602761310.42665267001357.246276366129.916608802633.5064395852
60.8165300482480.6439670579280.3429720528410.9008602164430.9354420706282.941801411180.29283399445-0.2388710390040.1744814412290.171773363244-0.2040633958920.059877282944-0.286020574552-0.640553177262-0.00836766219010.7836280238750.1360230837260.1222254182880.803434343637-0.240901330640.98787764734449.674216369134.765018490142.5194257432
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 467 )
3X-RAY DIFFRACTION3chain 'A' and (resid 468 through 758 )
4X-RAY DIFFRACTION4chain 'B' and (resid 99 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 116 )

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