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- PDB-1mzf: Human Factor inhibiting HIF (FIH1) in Complex with 2-oxoglutarate -

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Basic information

Entry
Database: PDB / ID: 1mzf
TitleHuman Factor inhibiting HIF (FIH1) in Complex with 2-oxoglutarate
Componentsfactor inhibiting HIF1
KeywordsOXIDOREDUCTASE / beta-jellyroll
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 / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / positive regulation of vasculogenesis / carboxylic acid binding / ankyrin repeat binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / positive regulation of vasculogenesis / carboxylic acid binding / ankyrin repeat binding / Notch binding / oxygen sensor activity / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / 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. / JmjC domain / JmjC domain profile. / Jelly Rolls / 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. / JmjC domain / JmjC domain profile. / Jelly Rolls / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDann III, C.E. / Bruick, R.K. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor 1: An Asparaginyl Hydroxylase Involved in the Hypoxic Response Pathway.
Authors: Dann III, C.E. / Bruick, R.K. / Deisenhofer, J.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: factor inhibiting HIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6583
Polymers40,4561
Non-polymers2022
Water90150
1
A: factor inhibiting HIF1
hetero molecules

A: factor inhibiting HIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3176
Polymers80,9132
Non-polymers4044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/41
2
A: factor inhibiting HIF1
hetero molecules

A: factor inhibiting HIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3176
Polymers80,9132
Non-polymers4044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4260 Å2
ΔGint-53 kcal/mol
Surface area31750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.460, 86.460, 147.810
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 factor inhibiting HIF1 / FIH-1


Mass: 40456.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIH-1 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9NWT6
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 294 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: potassium tartrate, CAPSO, iron(II) sulfate, 2-oxoglutarate, glycerol, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
350 mM1dropNaCl
45 mM2-mercaptoethanol1drop
550 mMCAPSO1reservoirpH9.6
60.9-1.2 Mpotassium tartrate1reservoir
730 %glycerol1reservoir
85 mM1reservoirFeSO4
920 mM2-OG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2002
RadiationMonochromator: Si grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.4→47.11 Å / Num. all: 22616 / Num. obs: 21549 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44 Å2 / Limit h max: 36 / Limit h min: 0 / Limit k max: 25 / Limit k min: 0 / Limit l max: 61 / Limit l min: 0 / Observed criterion F max: 527737.13 / Observed criterion F min: 0.32 / Rsym value: 0.076 / Net I/σ(I): 21.8
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 5.1 / Num. unique all: 2194 / Rsym value: 0.437 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Num. obs: 21793 / % possible obs: 98.2 % / Num. measured all: 172309 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.443

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Processing

Software
NameVersionClassificationNB
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FIH-1

Resolution: 2.4→29.93 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1082 5 %RANDOM
Rwork0.232 ---
all0.235 22618 --
obs0.235 21549 95.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 51.8402 Å2 / ksol: 0.357607 e/Å3
Displacement parametersBiso max: 109.69 Å2 / Biso mean: 60.46 Å2 / Biso min: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1--4.03 Å20 Å20 Å2
2---4.03 Å20 Å2
3---8.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 11 50 2822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.2931344.90.29423560.0252757249090.3
2.51-2.640.2911204.30.29225120.0272776263294.8
2.64-2.810.2861314.70.28825350.0252797266695.3
2.81-3.020.26113950.26125610.0222775270097.3
3.02-3.330.261244.40.2626340.0232818275897.9
3.33-3.810.2181334.70.21726360.0192823276998.1
3.81-4.790.1991495.20.19826030.0162868275295.9
4.79-29.930.25315250.25326300.023024278292
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 DIFFRACTION4akg.paramakg.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.28

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