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- PDB-1iz3: Dimeric structure of FIH (Factor inhibiting HIF) -

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Basic information

Entry
Database: PDB / ID: 1iz3
TitleDimeric structure of FIH (Factor inhibiting HIF)
ComponentsFIH
KeywordsTRANSCRIPTION / double Beta-sheet helix
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 / cytoplasm / cytosol
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
Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLee, C. / Kim, S.-J. / Jeong, D.-G. / Lee, S.M. / Ryu, S.-E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of human FIH-1 reveals a unique active site pocket and interaction sites for HIF-1 and von Hippel-Lindau.
Authors: Lee, C. / Kim, S.J. / Jeong, D.G. / Lee, S.M. / Ryu, S.E.
History
DepositionSep 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: FIH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7292
Polymers40,6331
Non-polymers961
Water00
1
A: FIH
hetero molecules

A: FIH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4594
Polymers81,2672
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3450 Å2
ΔGint-51 kcal/mol
Surface area31630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.89, 86.89, 143.42
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis : -x, y, -z

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Components

#1: Protein FIH / factor inhibiting HIF1


Mass: 40633.320 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) / References: UniProt: Q9NWT6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.48 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.4M Lithium sulfate, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.4 Mlithium sulfate1reservoir
320 %PEG40001reservoir
40.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.979 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 9, 2002
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 25821 / Num. obs: 24716 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→50 Å / % possible all: 95.7
Reflection
*PLUS
Num. obs: 13563 / % possible obs: 95.9 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 89.7 % / Num. unique obs: 98205 / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1169 -random
Rwork0.23 ---
all0.236 25821 --
obs0.236 24716 95.7 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 5 0 2778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
LS refinement shellResolution: 2.8→50 Å
Refinement
*PLUS
Lowest resolution: 99 Å / Num. reflection all: 13563 / % reflection Rfree: 5 % / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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