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- PDB-2wa3: FACTOR INHIBITING HIF-1 ALPHA WITH 2-(3-hydroxyphenyl)-2-oxoaceti... -

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Basic information

Entry
Database: PDB / ID: 2wa3
TitleFACTOR INHIBITING HIF-1 ALPHA WITH 2-(3-hydroxyphenyl)-2-oxoacetic acid
ComponentsHYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
KeywordsOXIDOREDUCTASE / HYDROXYLASE / DIOXYGENASE / TRANSCRIPTION / TRANSCRIPTION ACTIVATOR/INHIBITOR / HYPOXIA
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
2-(3-HYDROXYPHENYL)-2-OXO-ETHANOIC ACID / : / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsConejo-Garcia, A. / Lienard, B.M.R. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J.
Citation
Journal: Bioorg. Med. Chem. Lett. / Year: 2010
Title: Structural basis for binding of cyclic 2-oxoglutarate analogues to factor-inhibiting hypoxia-inducible factor.
Authors: Conejo-Garcia, A. / McDonough, M.A. / Loenarz, C. / McNeill, L.A. / Hewitson, K.S. / Ge, W. / Lienard, B.M. / Schofield, C.J. / Clifton, I.J.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1Alpha
Authors: Elkins, J. / Hewitson, K.S. / McNeill, L. / Seibel, J. / Schlemminger, I. / Pugh, C. / Ratcliffe, P. / Schofield, C.J.
History
DepositionFeb 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)40,5503
Polymers40,3281
Non-polymers2222
Water1,51384
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)81,1016
Polymers80,6572
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3440 Å2
ΔGint-48.8 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.938, 86.938, 148.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR / FACTOR INHIBITING HIF1 / HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE / FACTOR INHIBITING HIF-1 / FIH-1


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-A29 / 2-(3-HYDROXYPHENYL)-2-OXO-ETHANOIC ACID


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-(3-HYDROXYPHENYL)-2-OXOACETIC ACID (A29): PUBCHEM CID 13548097

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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: 3.57 Å3/Da / Density % sol: 65.3 % / Description: NONE
Crystal growpH: 7.5
Details: 1.5 M AMMONIUM SULFATE, 100MM HEPES PH 7.5, 3% PEG400, 1MM FESO4, 28MG/ML PROTEIN, 10MM SUBSTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2004 / Details: RH COATED MIRROR
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.5→37.1 Å / Num. obs: 20426 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2N

1h2n


Resolution: 2.5→74.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.119 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1043 5.1 %RANDOM
Rwork0.20327 ---
obs0.20546 19325 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.121 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--1.1 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 13 84 2862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222879
X-RAY DIFFRACTIONr_bond_other_d0.0020.021988
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9483913
X-RAY DIFFRACTIONr_angle_other_deg1.37634816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9875338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60924.557158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47815475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9831517
X-RAY DIFFRACTIONr_chiral_restr0.1520.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.2330.2630
X-RAY DIFFRACTIONr_nbd_other0.2080.22026
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21374
X-RAY DIFFRACTIONr_nbtor_other0.0960.21503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1821.52140
X-RAY DIFFRACTIONr_mcbond_other0.1871.5671
X-RAY DIFFRACTIONr_mcangle_it1.45622724
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.35531444
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4614.51187
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 68 -
Rwork0.432 1414 -
obs--100 %
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)
10.72111.01310.59751.7867-0.17053.3026-0.22450.11550.4093-0.4946-0.08730.73950.0922-0.2830.31170.0834-0.0038-0.2374-0.1871-0.06990.62038.54631.56815.57
22.58651.40740.16123.21020.88664.0577-0.19560.452-0.2063-0.33590.38710.05220.160.0997-0.19150.1364-0.0193-0.1158-0.22550.00480.340823.20920.85813.003
31.61761.03971.1410.76070.23153.52880.0322-0.3616-0.03751.0624-0.12310.18460.5967-0.33860.0910.2067-0.04980.03720.10990.06680.285414.60819.04638.526
41.52610.20470.19872.81331.6811.37120.0009-0.1356-0.03290.06720.1906-0.09730.16010.0192-0.19150.0954-0.0347-0.1153-0.19530.01480.392924.05123.623.308
52.0146-0.01871.45474.5959-0.50684.19190.0431-0.1370.1224-0.0489-0.07370.3753-0.184-0.08720.03060.0176-0.0149-0.0712-0.2171-0.02360.414321.70143.32932.368
61.62961.74941.50762.71281.59431.80860.0298-0.0393-0.0361-0.14540.0521-0.06210.21720.1983-0.08190.03130.0117-0.0705-0.1427-0.00330.38530.3435.30429.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 44
2X-RAY DIFFRACTION2A45 - 77
3X-RAY DIFFRACTION3A78 - 162
4X-RAY DIFFRACTION4A163 - 224
5X-RAY DIFFRACTION5A225 - 261
6X-RAY DIFFRACTION6A262 - 349

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