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- PDB-6ey1: prolyl hydroxylase from Trichoplax adhaerens -

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Basic information

Entry
Database: PDB / ID: 6ey1
Titleprolyl hydroxylase from Trichoplax adhaerens
ComponentsHIF prolyl hydroxylase
KeywordsOXIDOREDUCTASE / Prolyl hydroxylase / oxygenase / oxygen sensing / hypoxia inducible factor
Function / homology
Function and homology information


L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase ...Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / HIF prolyl hydroxylase
Similarity search - Component
Biological speciesTrichoplax adhaerens (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.199 Å
AuthorsMcDonough, M.A. / Boleininger, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Hypoxia (Auckl) / Year: 2018
Title: Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens.
Authors: Lippl, K. / Boleininger, A. / McDonough, M.A. / Abboud, M.I. / Tarhonskaya, H. / Chowdhury, R. / Loenarz, C. / Schofield, C.J.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIF prolyl hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5366
Polymers29,2121
Non-polymers3245
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-12 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.579, 59.413, 51.202
Angle α, β, γ (deg.)90.000, 100.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIF prolyl hydroxylase


Mass: 29212.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: PHD / Plasmid: pET28a(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I6QVT6
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.08 Å3/Da / Density % sol: 40.75 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200nl seeded drops, 20mg/ml protein sample, 2mM MN(II)CL2, 0.2M ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 / Details: mirrors
RadiationMonochromator: Si(III) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.199→39.868 Å / Num. obs: 74261 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 13.03 Å2 / Rmerge(I) obs: 0.084 / Χ2: 0.974 / Net I/σ(I): 25.9
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2 / Num. unique obs: 7022 / Χ2: 0.882 / % possible all: 94.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G1M

2g1m


Resolution: 1.199→39.868 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.41
RfactorNum. reflection% reflectionSelection details
Rfree0.1381 3738 5.04 %RANDOM
Rwork0.1216 ---
obs0.1225 74193 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.41 Å2 / Biso mean: 22.7044 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.199→39.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 19 199 1897
Biso mean--32.46 35.99 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111880
X-RAY DIFFRACTIONf_angle_d1.0862571
X-RAY DIFFRACTIONf_chiral_restr0.087274
X-RAY DIFFRACTIONf_plane_restr0.009339
X-RAY DIFFRACTIONf_dihedral_angle_d12.383725
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.199-1.21410.25471180.22242273239188
1.2141-1.23010.21671200.20732523264394
1.2301-1.2470.24841370.19252526266398
1.247-1.26480.19121310.17572634276599
1.2648-1.28370.17921490.168726052754100
1.2837-1.30370.1841330.143526172750100
1.3037-1.32510.16921260.141926192745100
1.3251-1.3480.16141400.129526352775100
1.348-1.37250.15681430.121225952738100
1.3725-1.39890.16681390.11526362775100
1.3989-1.42740.13341400.107826322772100
1.4274-1.45850.16151220.101426222744100
1.4585-1.49240.13561460.104126192765100
1.4924-1.52970.1291340.097926062740100
1.5297-1.57110.12711470.092626422789100
1.5711-1.61730.12971450.089226182763100
1.6173-1.66950.11031510.08826002751100
1.6695-1.72920.12491440.090226222766100
1.7292-1.79840.11661450.099126392784100
1.7984-1.88030.14581360.100226112747100
1.8803-1.97940.12361260.094726812807100
1.9794-2.10340.10011250.099426362761100
2.1034-2.26580.10621460.103326292775100
2.2658-2.49380.12141520.107626162768100
2.4938-2.85450.11751400.123626702810100
2.8545-3.59610.13831500.130326522802100
3.5961-39.89020.16441530.152126972850100

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