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- PDB-5jwl: Factor Inhibiting HIF D201E in Complex with Zn, and Alpha-Ketoglu... -

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Basic information

Entry
Database: PDB / ID: 5jwl
TitleFactor Inhibiting HIF D201E in Complex with Zn, and Alpha-Ketoglutarate
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / Hypoxia Inducible Factor / Factor Inhibiting HIF / Oxygenase / 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
2-OXOGLUTARIC ACID / DI(HYDROXYETHYL)ETHER / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTaabazuing, C.Y. / Garman, S.C. / Eron, S. / Knapp, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008515 United States
CitationJournal: To Be Published
Title: Factor Inhibiting HIF D201E in Complex with Zn, and Alpha-Ketoglutarate
Authors: Hangasky, J.A. / Taabazuing, C.Y. / Martin, C. / Eron, S. / Garman, S.C. / Knapp, M.J.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 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

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)41,1346
Polymers40,6251
Non-polymers5105
Water2,054114
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)82,26912
Polymers81,2492
Non-polymers1,02010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)86.131, 86.131, 149.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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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: 40624.578 Da / Num. of mol.: 1 / Mutation: D201E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Plasmid: pET28a / 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 , 5 types, 119 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 114 / 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: 63.9 % / Mosaicity: 0.795 °
Crystal growTemperature: 293 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: NSLS / Beamline: X6A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 3, 2013 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22314 / % possible obs: 98.2 % / Redundancy: 9 % / Rmerge(I) obs: 0.131 / Χ2: 2.276 / Net I/av σ(I): 27.048 / Net I/σ(I): 9.2 / Num. measured all: 201011
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.4-2.449.51100
2.44-2.499.511000.989
2.49-2.539.511000.907
2.53-2.599.511000.753
2.59-2.649.511000.751
2.64-2.79.511000.649
2.7-2.779.511000.503
2.77-2.859.511000.408
2.85-2.939.411000.345
2.93-3.029.411000.271
3.02-3.139.311000.232
3.13-3.269.311000.201
3.26-3.419.111000.165
3.41-3.589199.70.139
3.58-3.818.8199.70.129
3.81-4.18.41990.112
4.1-4.527.7195.60.106
4.52-5.177.8193.80.101
5.17-6.518.6197.90.099
6.51-507.5181.40.082

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D8C

3d8c


Resolution: 2.4→32.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.043 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.229
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1592 7.8 %RANDOM
Rwork0.1803 ---
obs0.1839 18715 89.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 165.11 Å2 / Biso mean: 67.601 Å2 / Biso min: 33.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0 Å20 Å2
2---1.03 Å20 Å2
3---2.06 Å2
Refinement stepCycle: final / Resolution: 2.4→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 28 114 2940
Biso mean--77.48 57.71 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192903
X-RAY DIFFRACTIONr_bond_other_d0.0010.022662
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9543937
X-RAY DIFFRACTIONr_angle_other_deg0.88936133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47524.551156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1315477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0171517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_mcbond_it4.2514.8911363
X-RAY DIFFRACTIONr_mcbond_other4.2514.8911362
X-RAY DIFFRACTIONr_mcangle_it6.3347.3151702
Refine LS restraints NCSNumber: 5447 / Type: TIGHT THERMAL / Rms dev position: 0 Å / Weight position: 0.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 103 -
Rwork0.212 1213 -
all-1316 -
obs--79.9 %
Refinement TLS params.Method: refined / Origin x: -15.3779 Å / Origin y: 21.5591 Å / Origin z: -9.3437 Å
111213212223313233
T0.0574 Å20.0109 Å2-0.0007 Å2-0.3366 Å20.1181 Å2--0.0583 Å2
L1.3686 °2-0.4849 °20.9324 °2-0.3074 °2-0.2399 °2--0.7104 °2
S0.0062 Å °-0.0469 Å °0.1022 Å °0.0811 Å °-0.0297 Å °-0.0605 Å °0.0554 Å °-0.1283 Å °0.0235 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 349
2X-RAY DIFFRACTION1A401 - 402

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