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- PDB-7a1m: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-propyl... -

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Basic information

Entry
Database: PDB / ID: 7a1m
TitleFACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-propyl-2-oxoglutarate
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / Hypoxia-inducible factor asparagine hydroxylase / Dioxygenase
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
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. / RmlC-like jelly roll fold
Similarity search - Domain/homology
3-propyl-2-oxoglutarate / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2021
Title: 2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases.
Authors: Nakashima, Y. / Brewitz, L. / Tumber, A. / Salah, E. / Schofield, C.J.
History
DepositionAug 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)40,8706
Polymers40,3281
Non-polymers5425
Water1,11762
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)81,74012
Polymers80,6572
Non-polymers1,08410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4310 Å2
ΔGint-171 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.954, 85.954, 148.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#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 / Production host: Escherichia coli BL21(DE3) (bacteria)
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QVW / 3-propyl-2-oxoglutarate / (3~{S})-2-oxidanylidene-3-propyl-pentanedioic acid


Mass: 188.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 63.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.178→74.448 Å / Num. obs: 51777 / % possible obs: 93.7 % / Redundancy: 25.8 % / Biso Wilson estimate: 55.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.156 / Net I/σ(I): 17.1
Reflection shellResolution: 2.178→2.216 Å / Redundancy: 24.2 % / Rmerge(I) obs: 6.807 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1487 / CC1/2: 0.414 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2K

1h2k


Resolution: 2.18→56.29 Å / SU ML: 0.4303 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 2487 4.8 %
Rwork0.2204 49290 -
obs0.2216 51777 92.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.38 Å2
Refinement stepCycle: LAST / Resolution: 2.18→56.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 0 62 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312866
X-RAY DIFFRACTIONf_angle_d0.58533909
X-RAY DIFFRACTIONf_chiral_restr0.0465396
X-RAY DIFFRACTIONf_plane_restr0.004521
X-RAY DIFFRACTIONf_dihedral_angle_d17.95061059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.220.48161370.46412712X-RAY DIFFRACTION92.23
2.22-2.220.492816X-RAY DIFFRACTION26.23
2.27-2.310.44681540.38792814X-RAY DIFFRACTION97.54
2.31-2.370.39021440.36352915X-RAY DIFFRACTION99.8
2.37-2.430.33241570.3352912X-RAY DIFFRACTION99.9
2.43-2.490.36071270.30143017X-RAY DIFFRACTION100
2.49-2.570.28581530.29672934X-RAY DIFFRACTION99.94
2.57-2.650.2981460.30152931X-RAY DIFFRACTION100
2.65-2.740.36921520.292958X-RAY DIFFRACTION99.84
2.74-2.850.28851410.26312917X-RAY DIFFRACTION99.93
2.85-2.980.27721470.23422984X-RAY DIFFRACTION100
2.98-3.140.26711580.23842917X-RAY DIFFRACTION99.87
3.14-3.340.24971450.23232958X-RAY DIFFRACTION99.97
3.34-3.60.25461200.21852969X-RAY DIFFRACTION99.71
3.6-3.960.22451310.19122509X-RAY DIFFRACTION84.91
3.96-4.530.20111750.16572945X-RAY DIFFRACTION100
4.53-5.710.19851580.17382916X-RAY DIFFRACTION100
5.71-56.290.22141420.20912966X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.029704959340.7741323448750.09140788535410.30229797378-0.03534813762380.788556333728-0.09600150775010.0210307494556-0.062381570366-0.832277178049-0.3333866627461.01715391231-0.419791694412-0.312287107670.2990022602010.949928414899-0.0143956870498-0.3031143029280.652368141845-0.02372737562771.0637922448810.465092963429.395205213814.3041538989
21.76244025098-0.416623393417-0.05136389675393.053472605951.095173079642.24029928964-0.0492359856882-0.107295117245-0.2075393224790.129035516392-0.06647568708460.271854560420.17365074753-0.01058402513260.07648313538880.731190859113-0.0653278568294-0.1056715558060.4819790497290.0372805271830.6871626989418.79924615819.276821780325.2249998554
30.440879505324-0.1693266280910.6219517470540.138125750835-0.3365361552340.9279330703740.432953174176-1.578224958050.09355853090421.24611941584-0.9338209001150.04828768891840.0657969108509-0.1969080805240.4786181622461.1553035323-0.1451548031310.05515005580711.038120875660.03780011958580.79399612606520.491947178127.17992376746.496734412
40.7755605077610.08838313999340.5108774184911.646803751120.07496222373671.94172463601-0.0632783442606-0.212295994457-0.5676439614590.680267795446-0.1203392089810.4777976102850.733375724856-0.4411926606780.01047844500250.993447483447-0.1914046033350.03896073134050.6652711822980.05405082899190.73723853618212.133013285512.89528221434.1220820694
52.882847734651.151779386720.7309419195772.331960060660.5237198270031.09974435765-0.02718721979910.1001378922390.001430829266550.1565396492530.31681490751-0.2218960732220.2240008882650.43856640265-0.4053328938890.8579704228030.0292784896066-0.124439058840.541502819212-0.03582231083530.78922687980829.689732378516.77342458721.0842465703
60.3987029504820.398650471780.7717174363991.716403846180.5041125474012.244984819480.0150841862008-0.1985433580510.1929536608920.136290991014-0.06831191119410.314629855436-0.0611167387276-0.07705694338090.04809445365150.708147395202-0.0257515189094-0.1215984826810.5271161506070.003515161976940.70478024394120.909902536233.17934806829.3326214132
70.310328167859-0.921366478258-0.101653723832.68150101280.3540587492920.652697724523-0.03828913140060.02770162279480.1039429122960.03079698329370.05435048730860.1230326604420.0186946509693-0.161185989062-0.006765938555930.774724076753-0.0346169424693-0.0947529944480.508904024096-0.01152062915950.7473516523218.903255846131.937470456424.4225670069
81.241181181510.124215767509-0.2563768301421.735593475490.8721381719720.401841853458-0.01266701120260.03540864638680.02201830176610.2203033977060.0565266046905-0.2247708282850.4546379544650.359326886972-0.1359374507310.7171899699960.00726302836832-0.1113998716740.672586548147-0.06568143901860.89184171410540.632853776136.567399313629.8682105376
94.054423589440.874750531215-0.474828326974.158346460910.03266918484412.76377044162-0.0673397324523-0.4478919476850.5875884220630.2182795566240.250563648920.5974846869810.471870547425-0.311509156216-0.08294679536120.68235213457-0.0578885154793-0.03057442807230.72921775335-0.032301088560.60063793659937.370082609749.720581698242.3625546791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 297 )
8X-RAY DIFFRACTION8chain 'A' and (resid 298 through 330 )
9X-RAY DIFFRACTION9chain 'A' and (resid 331 through 349 )

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