[English] 日本語
Yorodumi
- PDB-5jz6: Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jz6
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and L-malate
ComponentsAspartyl/asparaginyl beta-hydroxylase
KeywordsOXIDOREDUCTASE / 2-oxoglutarate dependent oxygenase / aspartyl/asparaginyl beta-hydroxylase / EGF-like domain hydroxylase / double stranded beta-helix / tetratricopeptide repeat
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 / positive regulation of intracellular protein transport / pattern specification process / 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 / detection of calcium ion / regulation of cytosolic calcium ion concentration / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / regulation of protein stability / calcium ion transmembrane transport / Stimuli-sensing channels / transmembrane transporter binding / electron transfer activity / cell population proliferation / negative regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / 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 / TPR repeat region circular profile. / TPR repeat profile. ...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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / : / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.354 Å
AuthorsMcDonough, M.A. / Pfeffer, I.
CitationJournal: Nat Commun / Year: 2019
Title: Aspartate/asparagine-beta-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern.
Authors: Pfeffer, I. / Brewitz, L. / Krojer, T. / Jensen, S.A. / Kochan, G.T. / Kershaw, N.J. / Hewitson, K.S. / McNeill, L.A. / Kramer, H. / Munzel, M. / Hopkinson, R.J. / Oppermann, U. / Handford, ...Authors: Pfeffer, I. / Brewitz, L. / Krojer, T. / Jensen, S.A. / Kochan, G.T. / Kershaw, N.J. / Hewitson, K.S. / McNeill, L.A. / Kramer, H. / Munzel, M. / Hopkinson, R.J. / Oppermann, U. / Handford, P.A. / McDonough, M.A. / Schofield, C.J.
History
DepositionMay 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9637
Polymers49,4051
Non-polymers5576
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.019, 70.641, 172.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1mM MMT buffer (DL-Malic acid, MES, Tris base), 25% PEG1500, 1 mM MnCl2, 2 mM N-oxalylglycine, 18 mg/ml protein

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.35→47.16 Å / Num. obs: 25633 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 35.39 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 14.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.354→47.153 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.2196 2000 7.82 %
Rwork0.1861 --
obs0.1888 25572 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.42 Å2 / Biso mean: 51.3736 Å2 / Biso min: 22.33 Å2
Refinement stepCycle: final / Resolution: 2.354→47.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 34 202 3698
Biso mean--60.49 42.77 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033573
X-RAY DIFFRACTIONf_angle_d0.6344817
X-RAY DIFFRACTIONf_chiral_restr0.032503
X-RAY DIFFRACTIONf_plane_restr0.002624
X-RAY DIFFRACTIONf_dihedral_angle_d14.8612152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3545-2.41340.32061390.24831634177399
2.4134-2.47860.31271410.233816601801100
2.4786-2.55150.251390.222116441783100
2.5515-2.63390.30111410.227216741815100
2.6339-2.7280.25671420.218916701812100
2.728-2.83720.23711410.209216501791100
2.8372-2.96630.24821430.212916911834100
2.9663-3.12270.25551400.192116521792100
3.1227-3.31830.2231430.189316911834100
3.3183-3.57440.2071430.179716811824100
3.5744-3.9340.21531430.159716871830100
3.934-4.50280.16921430.15151678182198
4.5028-5.67160.18461460.157917241870100
5.6716-47.16240.20551560.196218361992100
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)
13.9094-0.626-1.07514.15931.09374.3753-0.2737-1.17670.33641.72960.399-1.0089-0.31991.1209-0.15811.4257-0.1334-0.45021.2153-0.03871.0211-12.5088-9.812469.8123
22.6175-0.11790.37954.2797-2.34743.46150.0309-0.3817-0.1510.85370.022-0.2104-0.2508-0.1829-0.03760.5856-0.03590.00860.286-0.04780.4248-25.9344-7.476549.751
32.6467-0.8888-1.22721.30441.1672.07190.050.25450.0740.0680.0649-0.0496-0.10690.0413-0.10680.3232-0.0130.00980.294-0.04690.2993-11.33-3.10720.7043
43.3943-0.021-0.13681.62191.00421.82170.01010.3072-0.3710.17420.0504-0.13050.08440.0464-0.07080.2631-0.02460.00340.3656-0.09870.3355-4.5173-11.860914.3332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 392 )A330 - 392
2X-RAY DIFFRACTION2chain 'A' and (resid 393 through 500 )A393 - 500
3X-RAY DIFFRACTION3chain 'A' and (resid 501 through 624 )A501 - 624
4X-RAY DIFFRACTION4chain 'A' and (resid 625 through 758 )A625 - 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