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- PDB-6f0w: prolyl hydroxylase in complex with hypoxia inducible factor oxyge... -

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Basic information

Entry
Database: PDB / ID: 6f0w
Titleprolyl hydroxylase in complex with hypoxia inducible factor oxygen degradation domain peptide fragment from Trichoplax adhaerens
Components
  • HIF prolyl hydroxylase
  • Hypoxia inducible factor, alpha subunit
KeywordsOXIDOREDUCTASE / Prolyl hydroxylase / oxygenase / oxygen sensing / hypoxia inducible factor
Function / homology
Function and homology information


hypoxia-inducible factor-proline dioxygenase / L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / iron ion binding / regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
: / PAS fold-3 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / PAS fold / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type ...: / PAS fold-3 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / PAS fold / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / BHLH domain-containing protein / Hypoxia inducible factor, alpha subunit / hypoxia-inducible factor-proline dioxygenase
Similarity search - Component
Biological speciesTrichoplax adhaerens (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.301 Å
AuthorsMcDonough, M.A. / Boleininger, A. / Schofield, C.J.
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 20, 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 ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIF prolyl hydroxylase
S: Hypoxia inducible factor, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8974
Polymers31,6952
Non-polymers2022
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-18 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.841, 41.321, 42.076
Angle α, β, γ (deg.)114.060, 95.670, 103.690
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HIF prolyl hydroxylase


Mass: 29228.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: PHD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I6QVT6
#2: Protein/peptide Hypoxia inducible factor, alpha subunit


Mass: 2466.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Trichoplax adhaerens (invertebrata) / References: UniProt: I6QP75, UniProt: B3RXX2*PLUS
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.82 Å3/Da / Density % sol: 0.325 % / Description: rectangular rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20 mg/ml protein, 1mM MN(II)CL2, 2mM N-oxalylglycine, 10mM taHIF-ODD peptide, 0.31M ammonium acetate, 24% (w/v) PEG3350, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2010 / Details: MIRRORS
RadiationMonochromator: Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 55428 / % possible obs: 95.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.89 Å2 / Rmerge(I) obs: 0.112 / Χ2: 1.006 / Net I/σ(I): 8.5 / Num. measured all: 377792
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
1.3-1.354.153821.009192.3
1.35-1.44.954081.002192.6
1.4-1.466.254391.017193.6
1.46-1.547.355140.991194.4
1.54-1.647.755100.989194.40.765
1.64-1.767.855161.016195.30.462
1.76-1.947.856111.012195.70.23
1.94-2.227.756351.02196.80.13
2.22-2.87.756900.977197.60.094
2.8-506.857231.028198.40.065

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
GDAdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HQR

3hqr


Resolution: 1.301→37.478 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 2773 5 %RANDOM
Rwork0.1377 52640 --
obs0.1389 55413 94.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.77 Å2 / Biso mean: 20.6766 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.301→37.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 11 202 2066
Biso mean--13 33.74 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121997
X-RAY DIFFRACTIONf_angle_d1.1572725
X-RAY DIFFRACTIONf_chiral_restr0.081291
X-RAY DIFFRACTIONf_plane_restr0.011359
X-RAY DIFFRACTIONf_dihedral_angle_d13.687744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3009-1.32330.24841230.22012377250086
1.3233-1.34730.24581380.21152560269893
1.3473-1.37330.25421400.20352605274592
1.3733-1.40130.22621380.18582552269093
1.4013-1.43180.25271290.17232603273294
1.4318-1.46510.18851340.15942604273893
1.4651-1.50170.191380.15862603274194
1.5017-1.54230.17361430.13612631277495
1.5423-1.58770.19481360.12632619275594
1.5877-1.63890.14651350.12432628276395
1.6389-1.69750.16731410.11492649279095
1.6975-1.76550.15771370.11512626276395
1.7655-1.84580.14661440.11612654279896
1.8458-1.94320.14171400.1112680282096
1.9432-2.06490.14261410.11552702284397
2.0649-2.22430.13471390.11362666280597
2.2243-2.44810.14761430.12132695283897
2.4481-2.80230.15711440.13692733287798
2.8023-3.53010.13731450.13952714285999
3.5301-37.49360.17691450.15422739288498

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