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- PDB-5jza: Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR dom... -

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Basic information

Entry
Database: PDB / ID: 5jza
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and N-oxalylglycine
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 / pattern specification process / positive regulation of intracellular protein transport / activation of cysteine-type endopeptidase activity / face morphogenesis / structural constituent of muscle / positive regulation of calcium ion transport into cytosol / response to ATP / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / muscle contraction / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / cell population proliferation / transmembrane transporter binding / electron transfer activity / negative regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / 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
: / N-OXALYLGLYCINE / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)49,9767
Polymers49,4051
Non-polymers5706
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.730, 70.240, 170.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Plasmid: pET-28a(+) / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100 mM bicine, 100 mM sodium chloride, 27% PEG 550 MME, 1 mM manganese chloride, 2 mM N-oxalylglycine, 18 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→85.21 Å / Num. obs: 33179 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 46.25 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.6
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5APA

5apa


Resolution: 2.14→85.21 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.07
RfactorNum. reflection% reflection
Rfree0.1976 3748 6.05 %
Rwork0.1751 --
obs0.1765 33179 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.18 Å2 / Biso mean: 68.3722 Å2 / Biso min: 31.28 Å2
Refinement stepCycle: final / Resolution: 2.14→85.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 35 125 3622
Biso mean--77.08 56.79 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033574
X-RAY DIFFRACTIONf_angle_d0.7064818
X-RAY DIFFRACTIONf_chiral_restr0.033502
X-RAY DIFFRACTIONf_plane_restr0.004625
X-RAY DIFFRACTIONf_dihedral_angle_d15.1452154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.16710.29861390.25921482287100
2.1671-2.19560.27831390.264722142353100
2.1956-2.22570.26521340.25142109224399
2.2257-2.25750.26391400.24662164230499
2.2575-2.29120.27621380.235521542292100
2.2912-2.3270.26051380.22142171230999
2.327-2.36520.2461460.21392154230099
2.3652-2.4060.26061410.21632120226199
2.406-2.44970.21771440.20721932337100
2.4497-2.49680.21431380.19312152229099
2.4968-2.54780.21941360.195921572293100
2.5478-2.60320.25241420.20442190233299
2.6032-2.66380.21811380.19042115225399
2.6638-2.73040.2091380.18862181231999
2.7304-2.80420.20891410.18921592300100
2.8042-2.88670.26551350.20072152228799
2.8867-2.97990.26951380.1832159229799
2.9799-3.08640.20371410.182421462287100
3.0864-3.210.21121380.18342133227199
3.21-3.35610.21151390.17372166230599
3.3561-3.5330.18541420.1752183232599
3.533-3.75440.15281350.16312150228599
3.7544-4.04430.16421400.14592146228699
4.0443-4.45120.15891400.13762150229099
4.4512-5.09530.14011280.1442127225599
5.0953-6.41920.19191380.17652151228999
6.4192-85.27760.20541420.17132146228899
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)
12.44080.16091.24253.9523-0.23961.52140.26321.06130.3749-1.39950.1431-0.8189-0.70910.1433-0.67631.81090.24480.46511.7187-0.10521.0962-12.4968.3776-72.0983
28.63910.31831.07915.8978-0.62775.72090.08261.65760.6435-1.2675-0.2159-1.22660.25641.0575-0.05221.07770.12430.43210.9020.13641.0064-13.576514.5818-59.8962
32.0910.04920.31084.0843-2.05322.18370.04330.19410.1063-0.73420.01590.08230.2205-0.1855-0.04090.57740.022-0.00750.3207-0.08250.433-26.21752.1341-42.5452
43.99090.63031.14212.39181.81713.08550.1026-0.24850.0221-0.0480.1223-0.24720.05140.2131-0.23550.32340.03230.0120.3706-0.050.2942-4.78575.7846-16.2948
54.11470.1655-0.02762.51610.9042.46220.0112-0.22380.3581-0.1030.0228-0.0797-0.08410.0075-0.03160.25620.0356-0.01310.3715-0.09760.3192-7.291511.2522-12.3741
64.33590.4632-0.77561.98740.2693.83580.08640.07780.5295-0.42160.1809-0.3329-0.28230.4843-0.18940.40640.00230.05330.4603-0.0990.46722.326712.0382-22.3143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 374 )A330 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 410 )A375 - 410
3X-RAY DIFFRACTION3chain 'A' and (resid 411 through 538 )A411 - 538
4X-RAY DIFFRACTION4chain 'A' and (resid 539 through 616 )A539 - 616
5X-RAY DIFFRACTION5chain 'A' and (resid 617 through 734 )A617 - 734
6X-RAY DIFFRACTION6chain 'A' and (resid 735 through 758 )A735 - 758

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