[English] 日本語
Yorodumi
- PDB-7bmj: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -

+
Open data


ID or keywords:

Loading...

-
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 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
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more