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- PDB-2yc0: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE -

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Basic information

Entry
Database: PDB / ID: 2yc0
TitleFACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE
ComponentsHYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
KeywordsOXIDOREDUCTASE / DIOXYGENASE / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / ANKYRIN REPEAT DOMAIN / ARD / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / S-NITROSYLATION
Function / homology
Function and homology information


hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins ...Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2R)-2-hydroxypentanedioic acid / : / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChowdhury, R. / Clifton, I.J. / Schofield, C.J.
CitationJournal: EMBO Rep. / Year: 2011
Title: The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, ...Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, R.J. / Claridge, T.D. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A.
History
DepositionMar 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,47510
Polymers40,6111
Non-polymers8649
Water1,67593
1
A: HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
hetero molecules

A: HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,95020
Polymers81,2212
Non-polymers1,72918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6380 Å2
ΔGint-146.7 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.794, 86.794, 147.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR / FACTOR INHIBITING HIF-1 / FIH-1 / HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE


Mass: 40610.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase

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Non-polymers , 5 types, 102 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-2HG / (2R)-2-hydroxypentanedioic acid


Mass: 148.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.1 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES PH7.5, 1.6M AMMONIUM SULFATE, 6% PEG400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→42.84 Å / Num. obs: 29618 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.1
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2K

1h2k


Resolution: 2.15→42.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 216130.37 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1494 5 %RANDOM
Rwork0.241 ---
obs0.241 29618 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2205 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.34 Å20 Å20 Å2
2---4.34 Å20 Å2
3---8.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.15→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 49 93 2922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.382 181 5.7 %
Rwork0.332 2987 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4R2G.PARR2G.TOP
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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