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

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Basic information

Entry
Database: PDB / ID: 6yyu
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 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 / 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 / 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 / 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
2-OXOGLUTARIC ACID / : / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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

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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)49,6063
Polymers49,4051
Non-polymers2012
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-7 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.791, 70.003, 170.870
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
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 58.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES sodium, 10% v/v 2-Propanol, 20% w/v PEG 4000, 1 mM manganese chloride, 2 mM 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: 2.11→85.44 Å / Num. obs: 20459 / % possible obs: 90.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.185 / Net I/σ(I): 11
Reflection shellResolution: 2.11→2.42 Å / Rmerge(I) obs: 1.746 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1024 / CC1/2: 0.509 / % possible all: 56.2

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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: 2.11→85.44 Å / SU ML: 0.2308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2401
RfactorNum. reflection% reflection
Rfree0.2313 1064 5.2 %
Rwork0.2023 --
obs0.2039 20452 59.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.8 Å2
Refinement stepCycle: LAST / Resolution: 2.11→85.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 10 96 3410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01673410
X-RAY DIFFRACTIONf_angle_d1.61924630
X-RAY DIFFRACTIONf_chiral_restr0.0675496
X-RAY DIFFRACTIONf_plane_restr0.0099609
X-RAY DIFFRACTIONf_dihedral_angle_d21.80011237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.20.430250.345384X-RAY DIFFRACTION2.1
2.2-2.320.3425190.3421357X-RAY DIFFRACTION8.81
2.32-2.470.2697390.3093895X-RAY DIFFRACTION22.12
2.47-2.660.30461130.30062208X-RAY DIFFRACTION54.13
2.66-2.920.32672210.28393739X-RAY DIFFRACTION92.01
2.92-3.350.27672230.23474106X-RAY DIFFRACTION100
3.35-4.220.21961800.17243689X-RAY DIFFRACTION88.47
4.22-85.440.18652640.16984310X-RAY DIFFRACTION99.78

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