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- PDB-5apa: Crystal structure of human aspartate beta-hydroxylase isoform a -

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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 / 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 ryanodine-sensitive calcium-release channel activity / roof of mouth development / positive regulation of calcium ion transport into cytosol / 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 / 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 / regulation of protein stability / Stimuli-sensing channels / calcium ion transmembrane transport / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 4.47 Å3/Da / Density % sol: 72.52 % / Description: NONE
Crystal growDetails: 50MM SODIUM MALATE, 20% PEG3350, 3% DEXTRAN SULFATE, 20MM NISO4

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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

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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 )

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