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- PDB-4z1v: Structure of Factor Inhibiting HIF (FIH) in complex with Fe, NO, ... -

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Basic information

Entry
Database: PDB / ID: 4z1v
TitleStructure of Factor Inhibiting HIF (FIH) in complex with Fe, NO, and NOG
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / Hypoxia Inducible Factor / Factor Inhibiting HIF / Hydroxylase / Oxygen Sensing
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
: / NITRIC OXIDE / N-OXALYLGLYCINE / DI(HYDROXYETHYL)ETHER / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTaabazuing, C.Y. / Garman, S.C. / Knapp, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077413 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008515-17 United States
CitationJournal: Biochemistry / Year: 2016
Title: Substrate Promotes Productive Gas Binding in the alpha-Ketoglutarate-Dependent Oxygenase FIH.
Authors: Taabazuing, C.Y. / Fermann, J. / Garman, S. / Knapp, M.J.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Data collection
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,43010
Polymers40,6111
Non-polymers8199
Water1,78399
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)82,86020
Polymers81,2212
Non-polymers1,63918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area31300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.650, 86.650, 147.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Gene: HIF1AN, FIH1 / Plasmid: pET28a / Details (production host): Plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 6 types, 108 molecules

#2: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 1.6mM ammonium sulfate, 3% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→74.74 Å / Num. obs: 33489 / % possible obs: 99.6 % / Redundancy: 15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.025 / Net I/σ(I): 16 / Num. measured all: 503994 / Scaling rejects: 353
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.179.11.0921.92663029230.5010.36996.8
8.4-61.2712.80.03240.474175790.9990.00992.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALA0.2.8data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D8C

3d8c


Resolution: 2.1→74.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.477 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 3351 10 %RANDOM
Rwork0.1896 ---
obs0.1945 30068 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.5 Å2 / Biso mean: 56.428 Å2 / Biso min: 29.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.1→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 45 99 2904
Biso mean--79 51.21 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192884
X-RAY DIFFRACTIONr_bond_other_d0.0020.022598
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9583910
X-RAY DIFFRACTIONr_angle_other_deg0.91235979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3524.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37415454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5811515
X-RAY DIFFRACTIONr_chiral_restr0.1230.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02699
X-RAY DIFFRACTIONr_mcbond_it3.5383.8231364
X-RAY DIFFRACTIONr_mcbond_other3.5073.8231362
X-RAY DIFFRACTIONr_mcangle_it5.145.7111702
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 206 -
Rwork0.332 2125 -
all-2331 -
obs--95.61 %
Refinement TLS params.Method: refined / Origin x: -15.6884 Å / Origin y: 21.6157 Å / Origin z: -9.1673 Å
111213212223313233
T0.0579 Å2-0.0064 Å2-0.0011 Å2-0.288 Å20.0883 Å2--0.128 Å2
L1.423 °2-0.4339 °20.9983 °2-0.197 °2-0.2252 °2--0.8358 °2
S0.0297 Å °-0.1023 Å °0.133 Å °0.046 Å °-0.0289 Å °-0.0633 Å °0.084 Å °-0.1769 Å °-0.0009 Å °

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