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

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Basic information

Entry
Database: PDB / ID: 7bmj
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 5-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 / roof of mouth development / Protein hydroxylation / 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 / 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 / cellular response to calcium ion / muscle contraction / calcium ion transmembrane transport / regulation of protein stability / phospholipid binding / Golgi lumen / Stimuli-sensing channels / 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 / Alpha Horseshoe / Trypsin / 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
: / 5-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: 1.75 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

Downloads & links

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Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Coagulation factor X
C: Aspartyl/asparaginyl beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4817
Polymers103,0013
Non-polymers4804
Water6,323351
1
A: Aspartyl/asparaginyl beta-hydroxylase
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8364
Polymers53,5962
Non-polymers2402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-18 kcal/mol
Surface area19790 Å2
MethodPISA
2
C: Aspartyl/asparaginyl beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6453
Polymers49,4051
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-7 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.350, 59.480, 95.540
Angle α, β, γ (deg.)104.260, 91.510, 92.760
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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.: 2
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.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-U4Q / 5-fluoranylpyridine-2,4-dicarboxylic acid


Mass: 185.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4FNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein

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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: Sep 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.75→55.42 Å / Num. obs: 193533 / % possible obs: 96.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.35 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.122 / Net I/σ(I): 5.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 2.408 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5049 / CC1/2: 0.29 / % possible all: 95.7

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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: 1.75→46.26 Å / SU ML: 0.3102 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.7589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 9748 5.04 %
Rwork0.2208 183785 -
obs0.2224 193533 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.53 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7015 0 0 351 7366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457381
X-RAY DIFFRACTIONf_angle_d0.673210007
X-RAY DIFFRACTIONf_chiral_restr0.04231044
X-RAY DIFFRACTIONf_plane_restr0.00391317
X-RAY DIFFRACTIONf_dihedral_angle_d17.88232782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.60312900.5765618X-RAY DIFFRACTION84.26
1.77-1.790.57382830.56485812X-RAY DIFFRACTION86.87
1.79-1.810.55413280.54176090X-RAY DIFFRACTION90.65
1.81-1.840.53283320.52556267X-RAY DIFFRACTION91.55
1.84-1.860.50362980.5136062X-RAY DIFFRACTION91.62
1.86-1.890.49293300.4826286X-RAY DIFFRACTION93.29
1.89-1.910.4613390.47376356X-RAY DIFFRACTION93.79
1.91-1.940.48383420.46256189X-RAY DIFFRACTION93.65
1.94-1.970.4373760.4336291X-RAY DIFFRACTION93.61
1.97-20.40373380.41046187X-RAY DIFFRACTION93.05
2-2.040.41243420.38736296X-RAY DIFFRACTION93
2.04-2.070.34153600.35286216X-RAY DIFFRACTION93.57
2.07-2.110.34963490.32726218X-RAY DIFFRACTION93.33
2.11-2.160.33263410.31836316X-RAY DIFFRACTION93.66
2.16-2.20.33653290.29836293X-RAY DIFFRACTION93.53
2.2-2.260.2972910.27966304X-RAY DIFFRACTION92.89
2.26-2.310.30723050.26836293X-RAY DIFFRACTION93.88
2.31-2.380.29173550.25366281X-RAY DIFFRACTION93.57
2.38-2.440.28773310.24456242X-RAY DIFFRACTION93.93
2.44-2.520.25853220.23276243X-RAY DIFFRACTION92.91
2.52-2.610.26133280.22386305X-RAY DIFFRACTION92.98
2.61-2.720.24613090.21136261X-RAY DIFFRACTION92.98
2.72-2.840.25033300.20786183X-RAY DIFFRACTION92.67
2.84-2.990.22633110.21166098X-RAY DIFFRACTION91.06
2.99-3.180.29092950.20476149X-RAY DIFFRACTION90.66
3.18-3.430.20793410.1825946X-RAY DIFFRACTION89.03
3.43-3.770.22573470.16545795X-RAY DIFFRACTION86.43
3.77-4.310.16053190.1325747X-RAY DIFFRACTION86.43
4.31-5.430.16082600.13145914X-RAY DIFFRACTION87.06
5.44-46.260.17843270.16455527X-RAY DIFFRACTION83.06
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)
12.522338532650.37781895596-0.3738186656272.11799418211-0.6589356997633.881042888010.1320243794390.4710631356050.2291910167490.236389415001-0.005398843927890.283415744802-0.140007810646-0.531089106539-0.170181254760.5109149675720.1001866004020.127317256410.423058842521-0.01248556487150.4526321200227.350552923973.03528918032-73.3449352273
21.04194380318-0.2770183322390.192339796620.247677332333-0.2217756055854.21128440280.227816236686-0.0390774689810.2765799896120.0188735314195-0.288142528044-0.231992652573-0.361994029031.091280510960.06709191044230.576551682024-0.158071505620.07988391725540.7177903840970.152919674290.57647575459922.60346035225.52657801518-48.5324342219
31.75850349580.0503912437922-0.1619956533091.81774904928-0.5731473522821.87478330671-0.06672817684010.2429776765380.175159041125-0.1343740377440.1607878838610.0767877386724-0.240213713704-0.0973871464032-0.08886261084550.298578144677-0.0257541027514-0.0207066358820.3975660637660.003943875058020.3086609221196.09202105079-4.78706415616-23.1109492172
48.28432951846-0.0487799137321-4.070014739957.833565080630.4921887672372.033788294350.0382950701555-0.4919137069090.0520247157808-0.00180706012637-0.235444742044-0.2754507041280.04989123922540.364922081350.2491333821090.437300887383-0.07902273161360.01945473330270.7444028550910.1041806070550.52282215653612.226649044-5.0735095367-32.1363807455
54.32046554226-0.22982190536-3.667305758741.033752390040.7659955829818.403910841760.335770627121-0.1682234297670.0414002994312-0.143083337197-0.291050942793-0.31490561166-0.5069616056480.588976183712-0.1051687437720.509113218689-0.1671449729440.02631107650670.6856351561920.1856878693680.65971735694415.7517682710.6685286423-37.5293687371
66.737139323690.9464016859975.037823219273.888864452275.387722262069.66930490705-0.6475683078410.515484949749-0.0269949739533-0.598710180855-0.0466520582684-0.20081749562-0.004968814549380.3081208656360.5747182960120.790848094506-0.190274348060.05369527010320.7759021739650.03711414568220.4334139887599.52197663216-2.52774169639-43.4360697314
79.06545581054-5.904679951786.889019727199.85250207433-8.734840190038.57218469091-0.03181247615280.0848319809766-0.0128501784060.05960204195870.05985741264380.06511357950690.034190300232-0.0437023794217-0.01413415731810.680254467463-0.1741464527910.1508180629290.838313688448-0.0128334889070.5827388583461.97638508025-2.88353634367-53.6388187131
80.3581413797590.510166728290.4403877463252.0212687516-1.072718793043.729713850810.412558261602-0.3048729625610.2385507260810.105979342194-0.1779606671010.3828211315910.2750764141850.236399683829-0.08861392661580.95534720072-0.137570058730.07523064400820.6567903217750.09247181864450.981388129759-2.49283277725-29.5316034711-46.3743514451
91.732661778540.622161209671-0.04447040000550.6016276911120.1906410929622.837480399610.07977870612150.0192384652573-0.006006583495310.266073692719-0.23994145373-0.0808169353796-0.01701210725820.5070394709160.03987342253220.6672200788380.09334352704490.008072075598540.3995167381980.1408348555750.7413286523555.99702906425-26.228306868-76.0486923185
101.91837638641-0.8226131827520.2286035616432.83314000453-0.9545219479641.35799772991-0.0303906974408-0.137182018847-0.3611885525130.08778946838460.04412441354720.09504532009610.191212670481-0.0150520639774-0.02123276203620.347793378527-0.0246294455975-0.01709624031050.4160300052270.008704152485230.363671658053-16.3683137005-11.2519359389-94.876895083
112.05068445604-0.484249415844-0.3316989220792.20001087736-0.6659197386031.70758225376-0.0577636419758-0.0784989049261-0.1962666136350.139252289612-0.0352817355886-0.009475096607020.2022711921940.09220468565720.08409819647880.323155175278-0.00304583996717-0.02161520559650.3897410047790.01170422711050.342382849164-16.1469201422-5.56859315834-94.1054375629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 410 )
2X-RAY DIFFRACTION2chain 'A' and (resid 411 through 538 )
3X-RAY DIFFRACTION3chain 'A' and (resid 539 through 758 )
4X-RAY DIFFRACTION4chain 'B' and (resid 99 through 103 )
5X-RAY DIFFRACTION5chain 'B' and (resid 104 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 113 )
7X-RAY DIFFRACTION7chain 'B' and (resid 114 through 116 )
8X-RAY DIFFRACTION8chain 'C' and (resid 331 through 432 )
9X-RAY DIFFRACTION9chain 'C' and (resid 433 through 538 )
10X-RAY DIFFRACTION10chain 'C' and (resid 539 through 617 )
11X-RAY DIFFRACTION11chain 'C' and (resid 618 through 758 )

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