PDB-8y7p: Crystal structure of human GFOD1

ID or keywords:

Entry

Database: PDB / ID: 8y7p

Title

Crystal structure of human GFOD1

Components

Glucose-fructose oxidoreductase domain-containing protein 1

Keywords

OXIDOREDUCTASE / GFOD1 / glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family / glucose-fructose oxidoreductase / GFOR / GFOD

Function / homology

Function and homology information

Oxidoreductases / RHOQ GTPase cycle / oxidoreductase activity / nucleotide binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Zhang, T. / Shi, J.

Funding support

China, 2items

Citation

Journal: Acta Biochim.Biophys.Sin. / Year: 2024
Title: Molecular insight into the potential functional role of pseudoenzyme GFOD1 via interaction with NKIRAS2.
Authors: Shi, J. / Guo, X. / Liu, C. / Wang, Y. / Chen, X. / Wu, G. / Ding, J. / Zhang, T.

History

Deposition	Feb 4, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8y7p.cif.gz	279.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8y7p.ent.gz	226.7 KB	Display	PDB format
PDBx/mmJSON format	8y7p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8y7p_validation.pdf.gz	452.6 KB	Display	wwPDB validaton report
Full document	8y7p_full_validation.pdf.gz	456.8 KB	Display
Data in XML	8y7p_validation.xml.gz	28.2 KB	Display
Data in CIF	8y7p_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/8y7p ftp://data.pdbj.org/pub/pdb/validation_reports/y7/8y7p	HTTPS FTP

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Related structure data

Similar structure data	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	#35 - Nov 2002 Ferritin and Transferrin similarity (1)

Deposited unit

A: Glucose-fructose oxidoreductase domain-containing protein 1

B: Glucose-fructose oxidoreductase domain-containing protein 1

hetero molecules

86.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	184.940, 184.940, 58.073
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Glucose-fructose oxidoreductase domain-containing protein 1 Mass: 43288.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GFOD1, C6orf114 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NXC2, Oxidoreductases
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.28 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Hepes, pH 7.5, 2% (v/v) Tacsimate, and 20% (w/v) PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 10, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.6→47.01 Å / Num. obs: 22586 / % possible obs: 99.1 % / Redundancy: 4.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.076 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.6→2.65 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.875 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1127 / CC_1/2: 0.618

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AF-Q9NXC2

Resolution: 2.6→41.91 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2467	1131	5.01 %
R_work	0.1966	-	-
obs	0.1991	21449	97.34 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.6→41.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5222	0	6	31	5259

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	0
X-RAY DIFFRACTION	f_angle_d	0.575
X-RAY DIFFRACTION	f_dihedral_angle_d	13.868	1889
X-RAY DIFFRACTION	f_chiral_restr	0.043	860
X-RAY DIFFRACTION	f_plane_restr	0.007	925

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 (%)
2.6-2.66	0.3419	128	0.3419	2413	X-RAY DIFFRACTION	89
2.66-2.72	0.4104	139	0.3316	2646	X-RAY DIFFRACTION	98
2.72-2.79	0.4109	140	0.3195	2587	X-RAY DIFFRACTION	96
2.79-2.86	0.3519	129	0.2924	2655	X-RAY DIFFRACTION	98
2.86-2.95	0.3653	146	0.3018	2664	X-RAY DIFFRACTION	98
2.95-3.04	0.3377	133	0.2807	2622	X-RAY DIFFRACTION	97
3.04-3.15	0.3218	137	0.2603	2643	X-RAY DIFFRACTION	98
3.15-3.28	0.3192	144	0.2391	2625	X-RAY DIFFRACTION	97
3.28-3.42	0.3045	135	0.2479	2680	X-RAY DIFFRACTION	98
3.42-3.6	0.2585	143	0.1986	2676	X-RAY DIFFRACTION	99
3.61-3.83	0.2128	139	0.1734	2646	X-RAY DIFFRACTION	98
3.83-4.13	0.2298	144	0.1656	2689	X-RAY DIFFRACTION	98
4.13-4.54	0.1819	139	0.1602	2636	X-RAY DIFFRACTION	99
4.54-5.2	0.1705	138	0.152	2655	X-RAY DIFFRACTION	98
5.2-6.54	0.2746	143	0.183	2644	X-RAY DIFFRACTION	98
6.55-10	0.2053	144	0.154	2653	X-RAY DIFFRACTION	98

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	6.9731	-1.9281	-3.0835	8.7508	3.1786	8.7852	0.137	0.0412	-0.0093	0.0149	-0.0727	-0.6457	0.5821	0.3442	-0.0264	0.3957	0.065	0.0436	0.4176	0.0049	0.4034	-4.9928	-44.4604	-40.7356
2	1.925	-1.5681	-3.1894	4.5493	2.1289	4.967	0.863	1.1199	0.8626	-1.0864	-0.4717	-0.9592	-0.6832	-0.4841	-0.3407	0.71	0.2054	0.2459	0.7415	0.1689	0.6471	-11.9897	-26.6838	-42.7703
3	2.6157	-1.2797	-1.7459	6.6671	0.4246	6.0866	0.1612	0.2559	0.2656	0.1831	0.1144	-0.5921	-0.3031	-0.4561	-0.2262	0.3289	-0.0204	0.0534	0.5419	0.0147	0.3599	-19.6599	-24.8709	-25.7025
4	4.1547	-0.9707	-0.7989	4.877	1.9415	5.3147	0.2722	-0.0864	0.4414	-0.02	0.079	-1.4547	0.0964	0.3621	-0.3369	0.3454	0.0297	0.0536	0.5331	-0.0576	0.8341	-10.7392	-23.9123	-23.9832
5	3.9362	-2.2011	-0.3927	6.3234	1.0859	5.2771	0.1443	0.4486	0.5211	-0.1323	0.3369	-0.3641	-0.1837	-0.6649	-0.4513	0.3129	0.0476	0.0838	0.4797	0.0525	0.4516	-21.8799	-22.0691	-25.163
6	7.1692	-4.1988	-1.9833	2.4162	2.9011	4.0197	0.7545	1.276	-0.8565	-0.2175	-1.2388	1.3102	-0.1714	-1.5501	0.5514	0.6121	0.1956	-0.0083	1.1859	-0.153	0.5268	-33.6912	-24.5301	-32.2954
7	6.8546	-3.1988	-3.5623	9.1094	4.8384	2.0145	0.6939	1.8881	-0.5578	-0.8712	-1.0873	0.0711	0.08	-1.7865	0.5763	0.4683	0.0912	0.0427	0.9854	-0.02	0.6133	-20.6037	-36.5485	-42.4567
8	2.592	-0.599	0.2994	6.081	4.0585	2.8675	0.5517	1.3483	-0.775	-2.2129	-0.4811	-0.1006	-0.1114	-0.0528	0.2186	1.3986	0.552	0.2637	1.4193	0.0354	0.7022	-15.0593	-32.262	-53.7379
9	2.3649	-0.8925	-0.2338	4.0126	4.329	7.7248	0.0962	0.0755	0.6701	-0.4011	-0.1627	-0.6013	-0.6013	0.4972	0.1702	0.615	-0.0145	0.271	0.5879	0.0625	1.2856	-6.4823	-15.499	-30.1376
10	5.1382	-0.299	-4.0133	8.0574	1.4565	6.2339	0.1736	0.4385	0.1128	-0.349	-0.2526	1.2115	-0.1756	-1.1497	0.0345	0.3205	0.0397	-0.0618	0.6332	-0.0369	0.6135	-49.0098	-1.3006	-2.3423
11	5.9288	-1.5515	-1.9226	9.87	1.4467	4.6238	0.49	0.7726	0.3875	-1.1356	-0.8071	1.6085	-0.6832	-1.093	0.2543	0.6356	0.2134	-0.104	0.7827	-0.126	0.7536	-52.3737	8.5173	-3.3414
12	4.5297	-1.6897	-2.5746	7.0634	2.5782	6.7499	0.2627	-0.2855	0.4963	0.746	0.0437	-0.5688	-0.1071	0.0152	-0.2952	0.5486	-0.0043	-0.0258	0.3642	-0.0787	0.5474	-35.9776	5.8048	3.3408
13	3.2566	-2.1653	-1.4894	5.8897	3.0221	4.9722	0.0554	0.0427	0.3849	0.4253	0.0747	-0.5015	0.1312	-0.0135	-0.104	0.2805	-0.0533	-0.0134	0.3699	-0.0015	0.4095	-30.7609	-10.8684	-6.9518
14	4.5878	-2.7545	0.8671	6.9253	-0.2593	4.8997	0.4302	0.6537	1.1317	-0.6244	-0.393	-1.3781	-0.4557	0.3616	-0.0479	0.5016	-0.0318	0.2714	0.4744	0.0293	0.782	-24.7417	-3.5798	-19.0037
15	3.0705	-3.3848	-2.7804	7.8324	-0.2126	5.5466	0.0357	0.2756	0.5925	0.0802	-0.0594	-0.5877	-0.1446	-0.2232	0.0079	0.3063	-0.0351	0.0384	0.3174	0.0209	0.4294	-27.6155	-15.7114	-15.46
16	8.4301	-3.2193	-1.9004	6.8755	2.9627	6.3772	-0.6046	-0.0194	-0.9446	0.4872	0.2158	0.3697	1.2981	-0.2625	0.3288	0.7149	-0.081	0.0661	0.3864	0.0095	0.3361	-32.9781	-28.9645	-10.2014
17	6.8824	-3.6177	-6.709	7.7799	5.7109	8.1423	-0.2921	-0.1904	-0.9666	0.9833	-0.8104	0.7802	0.7225	-0.3714	0.9387	0.5438	-0.1173	0.0383	0.5237	-0.0044	0.5795	-44.1637	-11.8387	-0.2961
18	4.5144	-0.2866	-1.0581	8.9178	1.357	6.1988	0.0282	-0.9963	-0.0838	2.0394	0.1981	1.1228	0.8894	-0.6332	-0.1249	0.9417	-0.0988	0.0634	0.7337	0.0655	0.5251	-40.714	-9.0601	12.3294
19	6.7661	-1.8778	-4.0778	4.4461	1.6902	7.9143	0.2937	-0.5107	0.9895	-0.1338	0.1209	-1.5873	-0.7442	1.0742	-0.4026	0.4829	-0.0371	-0.0267	0.5582	-0.12	1.1446	-18.3455	-3.0235	-8.4452

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 86 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 87 through 137 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 138 through 161 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 162 through 227 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 228 through 252 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 253 through 299 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 300 through 317 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 318 through 336 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 337 through 364 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 24 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 25 through 54 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 55 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 188 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 189 through 227 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 228 through 253 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 254 through 299 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 300 through 317 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 318 through 336 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 337 through 363 )

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