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- PDB-4jaa: Factor inhibiting HIF-1 alpha in complex with consensus ankyrin r... -

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Basic information

Entry
Database: PDB / ID: 4jaa
TitleFactor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)LEU peptide
Components
  • CONSENSUS ANKYRIN REPEAT DOMAIN-(d)LEU
  • Hypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE/PEPTIDE / NON-HEME / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL / ASPARTYL HYDROXYLASE / EPIGENETIC REGULATION / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR/INHIBITOR / OXIDOREDUCTASE-PEPTIDE complex
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
N-OXALYLGLYCINE / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsScotti, J.S. / Ge, W. / McDonough, M.A. / Schofield, C.J.
CitationJournal: To be Published
Title: Structure of an oxygenase in complex with substrate
Authors: Scotti, J.S. / Ge, W. / McDonough, M.A. / Schofield, C.J.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.pdbx_leaving_atom_flag / _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_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
S: CONSENSUS ANKYRIN REPEAT DOMAIN-(d)LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9646
Polymers42,5602
Non-polymers4054
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-72 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.079, 86.079, 147.029
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 / Protein/peptide , 2 types, 2 molecules AS

#1: Protein Hypoxia-inducible factor 1-alpha inhibitor / Factor inhibiting HIF-1 / FIH-1 / Hypoxia-inducible factor asparagine hydroxylase


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase
#2: Protein/peptide CONSENSUS ANKYRIN REPEAT DOMAIN-(d)LEU


Mass: 2231.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide.

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Non-polymers , 4 types, 124 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.2 Å3/Da / Density % sol: 61.56 % / Mosaicity: 0.72 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.39→33.804 Å / Num. obs: 22451 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 44.565 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.3
Reflection shellResolution: 2.39→2.55 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3937 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å33.8 Å
Translation2.5 Å33.8 Å

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Processing

Software
NameVersionClassificationNB
SCALA0.1.16data scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2K
Resolution: 2.39→33.8 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8386 / SU ML: 0.28 / σ(F): 1.33 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 3688 9.25 %Random
Rwork0.184 ---
obs0.1873 22451 95.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 41.6862 Å2 / Biso min: 13.83 Å2
Refinement stepCycle: LAST / Resolution: 2.39→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 21 120 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012872
X-RAY DIFFRACTIONf_angle_d1.1423917
X-RAY DIFFRACTIONf_chiral_restr0.068404
X-RAY DIFFRACTIONf_plane_restr0.005517
X-RAY DIFFRACTIONf_dihedral_angle_d15.9041041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.3895-2.42090.31571290.294112861415141590
2.4209-2.45410.29691260.291212111337133782
2.4541-2.48910.28731260.290512601386138687
2.4891-2.52630.35821440.290513911535153595
2.5263-2.56580.27751480.252814261574157499
2.5658-2.60780.28071510.246314551606160699
2.6078-2.65280.25851420.25214351577157799
2.6528-2.7010.28611500.235414531603160399
2.701-2.75290.30471470.22914311578157899
2.7529-2.80910.24721460.218914321578157899
2.8091-2.87010.27231450.213214351580158098
2.8701-2.93680.23311470.212514401587158799
2.9368-3.01020.24781440.20714311575157598
3.0102-3.09160.22051460.20414551601160199
3.0916-3.18250.24041480.185514411589158999
3.1825-3.28510.22691470.192614221569156998
3.2851-3.40240.21521430.182114111554155496
3.4024-3.53850.19331260.175812261352135285
3.5385-3.69940.19591250.156212181343134383
3.6994-3.89420.1861410.159214291570157098
3.8942-4.13770.19661520.143114301582158299
4.1377-4.45660.16481520.136114381590159099
4.4566-4.90380.17281470.13214201567156798
4.9038-5.61060.2361390.159314101549154997
5.6106-7.05820.20231340.186913711505150593
7.0582-33.80760.19831430.178114231566156698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.3553-0.2112-1.5491.7150.17031.8714-0.07420.2009-0.3586-0.061-0.0388-0.07010.24340.0180.06760.18880.0324-0.02840.4135-0.18440.3369-22.008816.3239-17.3659
23.4451-1.22610.52853.46710.18262.8033-0.4208-1.0223-0.34850.96450.21960.10380.14190.20110.19390.49390.1421-0.01470.68380.04710.452-23.717113.38054.3056
33.654-0.5629-1.47460.74740.28872.40730.08970.0126-0.24240.1344-0.0087-0.03050.04810.0965-0.0660.14690.0233-0.03920.3651-0.12080.2877-27.237721.7177-10.81
44.8635-0.8884-1.82572.66410.57151.66-0.0237-0.02910.16960.00210.0824-0.17440.13640.0584-0.06480.27170.02830.03450.2611-0.07280.2588-41.37339.4848-2.451
54.11532.3519-0.30816.5838-2.52046.113-0.8325-0.43781.14350.48660.0042-0.4565-1.219-0.3630.77890.5236-0.0344-0.01060.4535-0.10520.4803-35.823846.758-6.7161
69.5077-6.3847-2.11244.34651.86153.15780.0021-0.69220.63261.0245-0.5084-0.6571-0.5987-0.39980.37520.4745-0.08150.03310.5005-0.23270.5178-27.095632.5602-3.3578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 22:95 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 96:149 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 150:297 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 298:349 )
5X-RAY DIFFRACTION5CHAIN S AND (RESID 791:796 )
6X-RAY DIFFRACTION6CHAIN S AND (RESID 797:806 )

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