[English] 日本語
Yorodumi
- PDB-5apa: Crystal structure of human aspartate beta-hydroxylase isoform a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5apa
TitleCrystal structure of human aspartate beta-hydroxylase isoform a
ComponentsASPARTYL/ASPARAGINYL BETA-HYDROXYLASE
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis ...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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis / pattern specification process / positive regulation of intracellular protein transport / activation of cysteine-type endopeptidase activity / face morphogenesis / structural constituent of muscle / response to ATP / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / muscle contraction / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / transmembrane transporter binding / cell population proliferation / electron transfer activity / 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 / NICKEL (II) ION / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.05 Å
AuthorsKrojer, T. / Kochan, G. / Pfeffer, I. / McDonough, M.A. / Pilka, E. / Hozjan, V. / Allerston, C. / Muniz, J.R. / Chaikuad, A. / Gileadi, O. ...Krojer, T. / Kochan, G. / Pfeffer, I. / McDonough, M.A. / Pilka, E. / Hozjan, V. / Allerston, C. / Muniz, J.R. / Chaikuad, A. / Gileadi, O. / Kavanagh, K. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
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
DepositionSep 15, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionSep 23, 2015ID: 3RCQ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Feb 21, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 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 / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)25,8974
Polymers25,6421
Non-polymers2553
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.221, 133.221, 44.637
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE / ASPARTATE BETA-HYDROXYLASE / ASP BETA-HYDROXYLASE / PEPTIDE-A SPARTATE BETA-DIOXYGENASE / ASPARTATE ...ASPARTATE BETA-HYDROXYLASE / ASP BETA-HYDROXYLASE / PEPTIDE-A SPARTATE BETA-DIOXYGENASE / ASPARTATE BETA-HYDROXYLASE


Mass: 25642.232 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 562-758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 4.47 Å3/Da / Density % sol: 72.52 % / Description: NONE
Crystal growDetails: 50MM SODIUM MALATE, 20% PEG3350, 3% DEXTRAN SULFATE, 20MM NISO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→19.87 Å / Num. obs: 28746 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 36.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.05→19.868 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 1442 5 %
Rwork0.1529 --
obs0.1546 28718 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→19.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 14 139 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071678
X-RAY DIFFRACTIONf_angle_d0.9942284
X-RAY DIFFRACTIONf_dihedral_angle_d13.749626
X-RAY DIFFRACTIONf_chiral_restr0.04241
X-RAY DIFFRACTIONf_plane_restr0.004297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12320.28621430.24952718X-RAY DIFFRACTION100
2.1232-2.20810.27391260.22152694X-RAY DIFFRACTION100
2.2081-2.30850.23331510.19392691X-RAY DIFFRACTION100
2.3085-2.430.18111320.17882734X-RAY DIFFRACTION100
2.43-2.58190.19521610.16132682X-RAY DIFFRACTION100
2.5819-2.78080.22971430.16992723X-RAY DIFFRACTION100
2.7808-3.05970.20391560.16162701X-RAY DIFFRACTION100
3.0597-3.50030.19691290.16382762X-RAY DIFFRACTION100
3.5003-4.40210.14441600.12532735X-RAY DIFFRACTION100
4.4021-19.86840.1661410.12912836X-RAY DIFFRACTION100
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)
11.34511.38490.97511.90360.18232.1873-0.14890.1686-0.4697-0.03370.1428-0.27140.15920.0457-0.00350.35760.00670.01460.3623-0.0170.546486.300133.23733.6785
23.86051.2169-1.76980.4713-0.1752.40490.07730.59950.9389-0.35580.2065-0.3609-0.64220.1957-0.17910.4509-0.13590.00480.48490.07140.500794.72156.20061.2855
32.5350.62250.09651.7774-0.06561.1455-0.22490.5080.2717-0.42540.17170.2232-0.28370.09010.03220.3707-0.0895-0.04130.41330.05060.392484.460649.3207-0.5467
42.0411.0746-0.15311.67340.2151.05420.0187-0.1762-0.1743-0.0062-0.0102-0.12840.05730.1075-0.00030.2664-0.0391-0.0060.32410.02780.361486.348142.69519.6791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 563 THROUGH 593 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 594 THROUGH 614 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 615 THROUGH 663 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 664 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