PDB-7a1j: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-(3-phe...

ID or keywords:

Entry

Database: PDB / ID: 7a1j

Title

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-(3-phenylpropyl)-2-oxoglutarate

Components

Hypoxia-inducible factor 1-alpha inhibitor

Keywords

OXIDOREDUCTASE / 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 / Notch binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Nakashima, Y. / Brewitz, L. / Schofield, C.J.

Citation

Journal: 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

Deposition	Aug 13, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 25, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 22, 2021	Group: 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 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7a1j.cif.gz	257.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7a1j_validation.pdf.gz	375.3 KB	Display	wwPDB validaton report
Full document	7a1j_full_validation.pdf.gz	376.4 KB	Display
Data in XML	7a1j_validation.xml.gz	16 KB	Display
Data in CIF	7a1j_validation.cif.gz	23.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a1/7a1j ftp://data.pdbj.org/pub/pdb/validation_reports/a1/7a1j	HTTPS FTP

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Related structure data

Related structure data	7a1kC 7a1lC 7a1mC 7a1nC 7a1oC 7a1pC 7a1qC 7a1sC 1h2kS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hl6-1 4bio-1 1mze-2 1h2l-1 3kcy-1 1h2n-1 6hl5-1 1iz3-1 2wa4-1 2wa3-1 3kcx-1 5o1m-d 1mzf-2 2w0x-1 6ha6-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (10) #122 - Feb 2010 Enhanceosome similarity (1)

Deposited unit

A: Hypoxia-inducible factor 1-alpha inhibitor

hetero molecules

41.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypoxia-inducible factor 1-alpha inhibitor

hetero molecules

A: Hypoxia-inducible factor 1-alpha inhibitor

hetero molecules

defined by author&software
Evidence: gel filtration
82.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.194, 86.194, 148.740
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
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

Components on special symmetry positions

ID	Model	Components
1	1	A-619- HOH
2	1	A-668- HOH

#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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-QVN / 3-(3-phenylpropyl)-2-oxoglutarate / (4~{S})-2-oxidanylidene-4-(3-phenylpropyl)pentanedioic acid Mass: 264.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.43 Å³/Da / Density % sol: 64.09 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97933 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 27, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 1.9→74.577 Å / Num. obs: 84236 / % possible obs: 100 % / Redundancy: 26.1 % / B_iso Wilson estimate: 55.21 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.056 / Net I/σ(I): 25.5
Reflection shell	Resolution: 1.9→1.933 Å / Redundancy: 28 % / R_merge(I) obs: 5.871 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2209 / CC_1/2: 0.308 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
xia2		data reduction
PHASER		phasing
autoPROC		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1H2K

1h2k

Resolution: 1.9→37.31 Å / SU ML: 0.2444 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2089	4234	5.03 %
R_work	0.1736	80002	-
obs	0.1754	84236	99.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 74.5 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→37.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2768	0	0	175	2943

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	2879
X-RAY DIFFRACTION	f_angle_d	1.3169	3926
X-RAY DIFFRACTION	f_chiral_restr	0.0868	396
X-RAY DIFFRACTION	f_plane_restr	0.0112	520
X-RAY DIFFRACTION	f_dihedral_angle_d	18.4049	1061

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.92	0.3969	133	0.3569	2622	X-RAY DIFFRACTION	98.46
1.92-1.94	0.2868	143	0.3474	2651	X-RAY DIFFRACTION	99.43
1.94-1.97	0.3546	148	0.3308	2691	X-RAY DIFFRACTION	99.86
1.97-1.99	0.3724	142	0.3211	2643	X-RAY DIFFRACTION	100
1.99-2.02	0.2452	115	0.3019	2682	X-RAY DIFFRACTION	99.93
2.02-2.05	0.3084	132	0.2803	2727	X-RAY DIFFRACTION	99.97
2.05-2.08	0.3016	171	0.263	2592	X-RAY DIFFRACTION	100
2.08-2.11	0.2273	133	0.2486	2695	X-RAY DIFFRACTION	99.93
2.11-2.14	0.2613	141	0.239	2681	X-RAY DIFFRACTION	100
2.14-2.18	0.274	157	0.2308	2648	X-RAY DIFFRACTION	100
2.18-2.21	0.2533	127	0.2012	2711	X-RAY DIFFRACTION	99.96
2.21-2.25	0.2234	140	0.1985	2635	X-RAY DIFFRACTION	100
2.25-2.3	0.2111	145	0.1859	2690	X-RAY DIFFRACTION	100
2.3-2.34	0.1781	141	0.1794	2660	X-RAY DIFFRACTION	100
2.34-2.39	0.2141	152	0.176	2658	X-RAY DIFFRACTION	100
2.39-2.45	0.2152	128	0.1801	2657	X-RAY DIFFRACTION	99.89
2.45-2.51	0.249	124	0.1955	2680	X-RAY DIFFRACTION	100
2.51-2.58	0.2076	114	0.1914	2683	X-RAY DIFFRACTION	100
2.58-2.65	0.2679	146	0.2068	2678	X-RAY DIFFRACTION	100
2.65-2.74	0.2819	162	0.2058	2656	X-RAY DIFFRACTION	100
2.74-2.84	0.2432	121	0.1988	2686	X-RAY DIFFRACTION	100
2.84-2.95	0.2137	155	0.1997	2663	X-RAY DIFFRACTION	100
2.95-3.09	0.1762	153	0.19	2653	X-RAY DIFFRACTION	100
3.09-3.25	0.2269	141	0.2018	2668	X-RAY DIFFRACTION	100
3.25-3.45	0.2457	166	0.187	2653	X-RAY DIFFRACTION	100
3.45-3.72	0.1996	134	0.166	2667	X-RAY DIFFRACTION	99.96
3.72-4.09	0.1387	118	0.1387	2704	X-RAY DIFFRACTION	100
4.09-4.68	0.1734	151	0.1191	2649	X-RAY DIFFRACTION	99.96
4.68-5.9	0.1957	158	0.1423	2643	X-RAY DIFFRACTION	100
5.9-37.31	0.2223	143	0.1867	2676	X-RAY DIFFRACTION	99.75

Refinement TLS params.

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

ID	L11 (°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)
1	1.78803515294	0.784260146775	-0.323589139789	0.666682388368	-0.365611097027	1.98719963056	-0.125356665187	0.415517232964	0.119113756923	-0.638353352285	-0.190760690647	0.93404764427	-0.0145253880657	-0.716354753334	0.312015128573	0.921798937949	-0.030273898569	-0.337051648433	0.681716663803	-0.047552347489	0.983273546461	10.5644146622	29.7061867943	14.1069201651
2	2.58808924671	0.188684840481	-0.127458807857	3.05869901057	2.36995647801	3.43832107318	-0.0443234411639	-0.0285219050452	-0.183548059248	0.0806371615655	-0.0498996019521	0.409525750193	0.466585588467	-0.168410371646	0.103665447309	0.758836225432	-0.0581205620408	-0.15825424693	0.456639648726	0.0721379566825	0.621010625839	19.1320995116	16.8064738826	22.3646134758
3	1.53812243203	0.421844322411	0.576505396864	1.49278301428	0.580409962504	2.93585936894	0.00172137368419	-0.606954905966	-0.0298261172993	0.664055144663	-0.146192791439	0.331209699255	0.518221055617	-0.347078275795	0.127731633672	1.00434515165	-0.150300922545	-0.00347559912734	0.645932497285	0.0517948517964	0.751227710385	15.0248642706	20.0717226709	38.1309686225
4	2.93887812533	1.20063875733	0.256662613983	2.93269178778	0.963030319012	1.99816636732	-0.00793546674986	0.0666947154044	-0.169663569943	-0.0870378662755	0.307791022115	-0.408600138031	0.52635381558	0.465223114711	-0.204561038226	0.811282952242	0.0169077237636	-0.154317492077	0.522923460168	0.00267987587965	0.669129875634	29.7118388164	17.1158825367	21.1184605869
5	1.2450398505	0.906304155187	1.17618216503	2.34599241497	1.17573060576	2.78772470581	0.000972673434051	-0.219232678747	0.13743215944	0.0567644899223	-0.0610476280889	0.455968035111	-0.0460307583447	-0.164313843559	0.0317691762494	0.709655644914	-0.0324074825017	-0.103847908804	0.470653863634	0.0245284632552	0.630129666497	20.9890925115	33.3435629453	29.1628086074
6	0.63372622061	0.00456218259023	-0.00294579519299	3.27086478845	1.42612532032	2.00256692012	-0.0712205297166	-0.0233880664234	0.0155260667293	-0.28728563634	0.0736577157653	0.457749212606	-0.0843901151285	-0.0920725621269	0.00830157955984	0.753065178855	-0.0361699691283	-0.138775156205	0.470356257726	0.0143171690743	0.656040091025	18.823379827	32.5266184719	24.4003920013
7	1.95176583485	0.47199554191	-0.196193105357	1.92150958263	0.793195474342	0.525835061299	-0.0215549757758	0.34873887627	-0.22485482438	-0.168762973578	0.123650355159	-0.33928383573	0.158740976908	0.537689252853	-0.205331066266	0.704531867961	0.0155012735828	-0.0963715639516	0.688879854746	-0.13256655224	0.746707266666	40.7084770222	36.8154872573	29.8064879981
8	3.88374522928	1.98330073634	-1.3629043397	9.00508849932	-3.24525384962	5.36740189986	0.0236919444959	-0.333103027381	0.422911481064	-0.0787403016172	0.166665095937	0.771913560259	0.633380686369	-0.318289698826	-0.102216216839	0.62335111253	-0.0580362960589	-0.0469278577542	0.750153952345	-0.070821237752	0.561857547402	37.2861545725	50.0430960138	42.3109952452

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 166 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 167 through 190 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 191 through 246 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 247 through 297 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 298 through 330 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 331 through 349 )

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