PDB-9hjs: Crystal structure of human geranylgeranyl diphosphate synthase mu...

ID or keywords:

Entry

Database: PDB / ID: 9hjs

Title

Crystal structure of human geranylgeranyl diphosphate synthase mutant R235C

Components

Geranylgeranyl pyrophosphate synthase

Keywords

TRANSFERASE / Multiple myeloma / GGPPS-R235C / geranylgeranyl diphosphate

Function / homology

Function and homology information

isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / isoprenoid biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.51 Å

Authors

Yehia, R. / Giladi, M. / Haitin, Y.

Funding support

Israel, 8items

Organization	Grant number	Country
Israel Science Foundation	1653/21	Israel
Israel Science Foundation	1721/16	Israel
Other private	ICRF 01214	Israel
Other private	ICRF 19202	Israel
Other private	Israel Cancer Association 20230029	Israel
Other private	Kahn Foundation's Orion project	Israel
Other private	Karl and Leonora Fingerhut Fund for Cancer Research	Israel
Other private	Recanati Foundation	Israel

Citation

Journal: To Be Published
Title: Crystal structure of human geranylgeranyl diphosphate synthase mutant R235C
Authors: Yehia, R. / Kadek, A. / Portasikova, J.M. / Man, P. / Giladi, M. / Haitin, Y.

History

Deposition	Dec 1, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hjs.cif.gz	689 KB	Display	PDBx/mmCIF format
PDB format	pdb9hjs.ent.gz	573.7 KB	Display	PDB format
PDBx/mmJSON format	9hjs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hj/9hjs ftp://data.pdbj.org/pub/pdb/validation_reports/hj/9hjs	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	#201 - Sep 2016 Isoprene Synthase similarity (8) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: Geranylgeranyl pyrophosphate synthase

B: Geranylgeranyl pyrophosphate synthase

C: Geranylgeranyl pyrophosphate synthase

D: Geranylgeranyl pyrophosphate synthase

E: Geranylgeranyl pyrophosphate synthase

F: Geranylgeranyl pyrophosphate synthase

hetero molecules

215 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	102.623, 69.081, 154.987
Angle α, β, γ (deg.)	90.00, 97.39, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	D-509- HOH

#1: Protein	Geranylgeranyl pyrophosphate synthase / GGPP synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase ...GGPP synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranylgeranyl diphosphate synthase / Geranyltranstransferase Mass: 35382.230 Da / Num. of mol.: 6 / Mutation: R235C Source method: isolated from a genetically manipulated source Details: Geranylgeranyl pyrophosphate synthase R235C / Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Production host: Escherichia coli (E. coli) References: UniProt: O95749, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical	ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE Mass: 450.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₀H₃₆O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.57 Å³/Da / Density % sol: 52.07 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium cacodylate pH 6.6, 40% MPD, 5% PEG 8000, 0.1M spermine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 2.51→48.327 Å / Num. obs: 56879 / % possible obs: 77.2 % / Redundancy: 3.5 % / CC_1/2: 0.999 / Net I/σ(I): 12.5
Reflection shell	Resolution: 2.51→2.699 Å / Num. unique obs: 2844 / CC_1/2: 0.5456

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.51→45.19 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2709	1999	3.52 %	Random
R_work	0.2269	-	-	-
obs	0.2284	56863	76.99 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.51→45.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13402	0	186	81	13669

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	13868
X-RAY DIFFRACTION	f_angle_d	0.791	18895
X-RAY DIFFRACTION	f_dihedral_angle_d	17.965	4823
X-RAY DIFFRACTION	f_chiral_restr	0.047	2156
X-RAY DIFFRACTION	f_plane_restr	0.009	2423

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 (%)
2.51-2.58	0.3387	9	0.3224	250	X-RAY DIFFRACTION	5
2.58-2.65	0.3012	44	0.3365	1179	X-RAY DIFFRACTION	23
2.65-2.72	0.3646	70	0.324	1967	X-RAY DIFFRACTION	39
2.72-2.81	0.357	99	0.3336	2690	X-RAY DIFFRACTION	53
2.81-2.91	0.4055	131	0.3383	3624	X-RAY DIFFRACTION	72
2.91-3.03	0.3717	160	0.3194	4396	X-RAY DIFFRACTION	86
3.03-3.17	0.3375	181	0.3015	4940	X-RAY DIFFRACTION	98
3.17-3.33	0.3279	184	0.2917	5065	X-RAY DIFFRACTION	100
3.33-3.54	0.3046	185	0.2713	5086	X-RAY DIFFRACTION	100
3.54-3.81	0.2779	185	0.2301	5077	X-RAY DIFFRACTION	100
3.82-4.2	0.2913	185	0.2069	5070	X-RAY DIFFRACTION	100
4.2-4.81	0.2089	187	0.1744	5129	X-RAY DIFFRACTION	100
4.81-6.05	0.3028	188	0.2298	5146	X-RAY DIFFRACTION	100
6.05-45.19	0.1995	191	0.1806	5245	X-RAY DIFFRACTION	99

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	2.3024	2.2902	-0.7596	1.9687	-0.35	0.3427	-0.1003	0.48	-0.6718	-0.2477	-0.4177	0.3741	0.3913	-0.9689	0.3962	0.9733	-0.0328	-0.3882	1.0892	-0.5297	1.6873	73.1559	60.0996	33.3983
2	0.8464	0.0694	0.6628	1.1343	-0.0465	1.7022	0.4495	-0.018	0.0609	0.0168	-0.3612	0.3346	0.3618	-0.4648	-0.0599	0.7638	0.0312	-0.2231	0.724	-0.4308	1.2517	80.7044	65.1714	36.5808
3	2.2795	0.0892	-1.2282	1.1977	-0.1345	1.3856	0.2397	0.4558	-0.3421	0.4449	-0.1003	0.1638	0.3757	-0.5464	-0.1632	0.8086	0.1366	-0.2647	1.1107	-0.4085	1.1287	71.3064	72.2195	30.6537
4	3.2125	-0.0314	1.0364	1.3821	-1.4236	1.5061	0.1961	0.0965	-0.9784	-0.094	-0.1266	0.4179	0.3618	-0.6559	-0.0581	0.5992	-0.0845	-0.0752	0.8425	-0.3792	1.1796	73.3951	69.5819	49.7319
5	0.7779	-1.6325	0.9283	3.818	-2.3513	2.0929	0.2745	-0.0117	-0.5004	-0.8271	0.2022	1.378	1.424	-0.1967	0.0051	0.7819	-0.0035	-0.1048	0.9096	-0.3296	1.3073	91.613	62.9026	50.3003
6	4.0787	0.0181	-2.153	0.8981	-1.79	4.9611	-0.0464	-1.109	0.4221	0.4705	-0.5477	0.7233	0.4311	0.96	0.0671	0.7521	-0.1534	0.1319	0.6667	-0.4015	1.2064	93.8006	71.2959	60.9044
7	7.3276	-0.1485	-3.5524	2.6915	0.0377	7.3865	0.5418	-1.576	-1.4039	1.2761	-0.515	0.3201	1.9817	0.2842	-0.121	0.7353	-0.2642	-0.1168	0.6275	-0.2694	1.0112	97.8909	62.8689	60.9549
8	4.2484	-0.6782	0.5939	1.3605	-0.8088	4.061	0.7374	-0.812	-1.8055	-0.6773	0.2313	-0.4054	0.8069	-1.2265	-0.7837	0.8992	-0.4028	0.0842	1.0765	-0.115	1.3349	74.588	57.4947	61.538
9	3.522	0.7065	-0.6739	0.2693	-0.5006	1.2995	-0.148	-0.1475	-0.8847	-0.6514	0.0318	-0.0035	0.6031	-0.056	0.0085	0.947	-0.3049	0.0589	0.9527	-0.4788	2.1089	72.2144	50.7569	53.4888
10	2.277	-0.8378	0.8147	1.4119	-0.053	2.4624	0.076	0.0398	0.0882	-0.2808	-0.2329	0.5286	-0.6491	-0.9256	0.1128	0.7696	0.2975	-0.2791	0.8329	-0.299	1.0938	76.9395	92.3568	33.7877
11	2.4972	-1.1723	1.0479	1.2387	-0.4975	2.2023	0.2231	0.6396	-0.0976	-0.2507	-0.3658	0.2488	0.0518	-0.4261	0.1496	0.8391	0.2934	-0.3042	0.9218	-0.3533	0.9668	76.569	85.1049	22.7326
12	4.2344	-0.3721	0.0615	2.4223	0.4615	2.1616	0.2599	0.5664	-0.0893	-0.6297	-0.1763	0.408	-0.1349	0.0189	-0.1479	1.0023	0.3659	-0.2219	0.7481	-0.1165	0.9364	100.5362	86.9089	17.0543
13	8.4326	-4.4933	-1.1848	2.8182	0.0521	1.1903	0.5814	1.0832	0.4653	-0.4709	-0.557	-0.0298	-0.4478	-0.2829	-0.1079	1.3127	0.4781	-0.3561	1.0015	-0.02	1.0821	80.829	100.4885	11.3317
14	2.1733	-0.1155	0.2685	3.7484	1.1152	3.9065	0.1119	-0.1653	0.1627	0.2519	-0.1836	-0.1211	-0.2884	0.4796	0.065	0.3611	-0.0895	0.1221	0.3884	-0.0429	0.4314	123.3379	95.7778	63.7105
15	2.0767	0.0375	0.6709	1.6655	0.4191	2.3619	0.0239	-0.0968	0.2678	0.0738	-0.2042	0.6114	-0.416	-0.2041	0.1757	0.5023	-0.0192	0.0911	0.4343	-0.1875	0.7685	103.0822	100.983	62.639
16	2.3041	-1.622	1.6594	1.8005	-0.9966	2.8563	0.0645	-0.4994	-0.0298	0.4995	0.0533	0.3199	-0.1067	-0.2107	-0.0722	0.502	-0.103	0.1202	0.3875	-0.0906	0.5102	115.9844	73.677	72.8404
17	2.4939	-0.2474	-0.5009	3.1193	-0.6594	1.6914	0.1599	-0.1681	0.1548	0.3996	-0.1682	-0.124	-0.2208	0.1789	0.0407	0.3143	-0.043	0.0101	0.3432	-0.0347	0.2854	131.2404	71.4257	66.6872
18	6.7871	-0.6603	0.3035	5.231	0.3549	4.8709	-0.0339	0.277	-0.2437	-0.181	-0.2939	0.3196	0.5683	-0.0385	0.2773	0.5464	0.1164	-0.0205	0.5445	-0.0542	0.3729	125.9961	64.2954	47.6308
19	1.8454	-1.0154	1.1929	2.9439	-1.3305	7.5979	0.3124	0.1675	-0.2889	-0.1312	-0.2568	0.0315	0.9666	0.4129	-0.0158	0.4158	0.0236	-0.0443	0.3852	-0.0785	0.4342	131.3216	55.3213	61.5809
20	1.1248	0.3943	0.4111	2.194	1.2775	2.518	0.2218	0.4795	-0.2341	-0.7902	-0.2247	0.0473	0.2466	0.5379	0.0109	0.9325	0.4073	-0.0777	0.7732	-0.0889	0.4455	128.9961	58.4428	20.1471
21	2.4899	-0.3654	-0.4966	0.7553	0.6866	1.9254	0.0768	0.3377	-0.2166	-0.4922	-0.2967	0.4012	0.4338	-0.0726	0.2287	1.2053	0.3738	-0.3138	0.7463	-0.2525	0.7843	109.6383	53.6203	15.7948
22	2.3117	1.6387	0.1628	2.6683	-1.0464	1.312	-0.2298	0.8422	0.0972	-0.6185	0.3418	0.304	-0.1287	0.0329	-0.1061	1.0371	0.1938	-0.0901	0.8621	-0.0238	0.5478	125.2347	84.3718	5.86
23	1.4307	-0.0089	-0.1357	2.4374	0.4038	1.3656	0.1193	0.6748	0.3554	-0.8731	-0.1595	-0.0531	-0.0945	0.27	0.0809	1.018	0.3923	-0.0618	0.8973	0.0881	0.4364	127.2706	77.3726	14.5448
24	0.9031	0.4266	0.3152	1.8533	-0.244	0.7671	0.0829	0.2605	-0.0461	-0.6741	-0.1177	-0.3259	0.1547	0.6261	0.0779	0.8965	0.336	0.0463	0.9043	0.1562	0.5085	138.5532	81.9702	20.5902
25	0.7586	0.7732	-0.8414	2.4622	1.2285	3.0775	0.7365	0.7906	0.5914	-1.4051	-0.3544	-0.7871	-0.1402	0.3385	-0.1672	0.9301	0.26	0.1529	0.9622	0.1888	0.5516	139.0967	90.71	17.7169
26	5.2888	-2.6014	1.8955	4.5843	-0.5628	2.3544	0.2457	0.6787	1.2708	-0.9824	-0.5337	-0.5722	-0.523	0.8782	0.2802	0.7121	0.2021	-0.0081	0.883	-0.069	0.7496	123.2551	91.2074	29.7063
27	4.385	-0.0133	-1.8833	2.9352	0.6755	5.6595	0.4586	0.207	0.4511	-0.2688	-0.2254	-0.0699	-0.6523	0.5915	-0.2118	0.4491	0.1216	0.0294	0.5843	0.1276	0.4213	133.8459	94.2755	34.3507
28	3.68	-0.7929	0.8455	6.0836	3.3059	2.2802	-0.4695	-0.2997	0.6196	1.1921	-0.4131	-0.8485	0.6322	1.011	0.8592	0.9408	0.1987	-0.0102	0.8459	0.219	0.6019	137.4844	100.7336	13.7926

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 84 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 110 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 111 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 214 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 215 through 240 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 241 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 256 through 278 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 279 through 296 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 84 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 85 through 194 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 195 through 255 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 256 through 296 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 3 through 110 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 111 through 298 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 5 through 110 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 111 through 194 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 195 through 240 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 241 through 297 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 4 through 110 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 111 through 296 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 3 through 42 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 43 through 134 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 135 through 166 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 167 through 194 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 195 through 214 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 215 through 278 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 279 through 296 )

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