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- PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -

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Basic information

Entry
Database: PDB / ID: 6yyv
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 3-methyl-2-oxoglutarate
ComponentsAspartyl/asparaginyl beta-hydroxylase
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 / 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 / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / Chem-Q1Z / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2020
Title: Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase.
Authors: Brewitz, L. / Nakashima, Y. / Schofield, C.J.
History
DepositionMay 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,6203
Polymers49,4051
Non-polymers2152
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-7 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.802, 70.521, 174.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-Q1Z / (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid


Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 200 mM magnesium acetate tetrahydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-2-oxoglutarate, 18 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.77→87.24 Å / Num. obs: 43399 / % possible obs: 94.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 32.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.1
Reflection shellResolution: 1.77→1.96 Å / Rmerge(I) obs: 1.876 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2170 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JZA

5jza


Resolution: 1.77→43.62 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5691
RfactorNum. reflection% reflection
Rfree0.2084 2111 4.86 %
Rwork0.1727 --
obs0.1745 43399 72.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.66 Å2
Refinement stepCycle: LAST / Resolution: 1.77→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 11 408 3811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01193511
X-RAY DIFFRACTIONf_angle_d1.14954759
X-RAY DIFFRACTIONf_chiral_restr0.0579503
X-RAY DIFFRACTIONf_plane_restr0.0087625
X-RAY DIFFRACTIONf_dihedral_angle_d21.71951307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.343560.273285X-RAY DIFFRACTION2.33
1.81-1.860.285380.2735175X-RAY DIFFRACTION4.77
1.86-1.910.2051230.2722523X-RAY DIFFRACTION13.94
1.91-1.960.3512630.26641323X-RAY DIFFRACTION35.42
1.96-2.030.25061140.23922050X-RAY DIFFRACTION55.13
2.03-2.10.28711440.23022818X-RAY DIFFRACTION75.75
2.1-2.180.26351900.21333709X-RAY DIFFRACTION98.93
2.18-2.280.22731910.19953743X-RAY DIFFRACTION99.9
2.28-2.40.23461840.18793770X-RAY DIFFRACTION99.97
2.4-2.550.20261710.17933801X-RAY DIFFRACTION100
2.55-2.750.21622140.19133759X-RAY DIFFRACTION99.97
2.75-3.030.22991960.18643810X-RAY DIFFRACTION99.98
3.03-3.470.25671720.17453837X-RAY DIFFRACTION100
3.47-4.360.17142060.13843862X-RAY DIFFRACTION100
4.37-43.620.17992290.15774023X-RAY DIFFRACTION99.86
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)
11.804136040630.6794712146751.486571997054.211057615130.5497023271491.50465685190.2220048022931.14644767976-0.0731030708531-1.71114899059-0.0148749498426-1.073656564440.2401421267110.626140899661-0.4328826221561.571381235150.3256555062760.4638185859981.41498573795-0.2938986987760.796670549456-13.59448347348.83377957262-72.8512310656
21.205577616-0.4206403753670.3164607719842.01750401565-1.110562642161.244700677460.139796775910.2478773666020.0438636827668-0.52814750535-0.14546543448-0.2057412863810.25185953907-0.00472344585544-0.01973895162450.4328514957180.04115924341520.009315359300490.129500221228-0.04455734202580.256625175928-24.49626060487.24863062573-49.4543052326
31.883198109540.4142384950740.6631442451920.8846612648970.5762693790421.336008472860.0148520309196-0.059114127672-0.226848988222-0.1049783213450.13473410578-0.1147398953350.1470918432760.194371606902-0.1016592822760.2340332596230.02427310564760.0005545550487190.20108297142-0.07241390377190.235680572663-6.90916852218-0.343930493646-24.2584906448
42.35526772380.1914401161040.2205429685481.001714198230.6224847534010.9924278912040.00890890401374-0.358523928340.274333898173-0.1519165010140.027209279492-0.0406667375325-0.1185592517690.0257353856575-0.05272414946380.1597004442160.0104178211379-0.003114623976660.25662160567-0.08475665699080.203314828912-6.0049051098213.4002513382-13.1719682759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 374 )
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 517 )
3X-RAY DIFFRACTION3chain 'A' and (resid 518 through 593 )
4X-RAY DIFFRACTION4chain 'A' and (resid 594 through 758 )

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