PDB-8ruw: Crystal structure of Archaeoglobus fulgidus (S)-3-O-geranylgerany...

ID or keywords:

Entry

Database: PDB / ID: 8ruw

Title

Crystal structure of Archaeoglobus fulgidus (S)-3-O-geranylgeranylglyceryl phosphate synthase

Components

Geranylgeranylglyceryl phosphate synthase

Keywords

TRANSFERASE / GGGPS

Function / homology

Function and homology information

phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Archaeoglobus fulgidus DSM 4304 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Eilert, L. / Blankenfeldt, W.

Funding support

Germany, 1items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Biocatalytic Ether Lipid Synthesis by an Archaeal Glycerolprenylase.
Authors: Kaspar, F. / Eilert, L. / Staar, S. / Oung, S.W. / Wolter, M. / Ganskow, C.S.G. / Kemper, S. / Klahn, P. / Jacob, C.R. / Blankenfeldt, W. / Schallmey, A.

History

Deposition	Jan 31, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 16, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ruw.cif.gz	747 KB	Display	PDBx/mmCIF format
PDB format	pdb8ruw.ent.gz	632 KB	Display	PDB format
PDBx/mmJSON format	8ruw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ruw_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	8ruw_full_validation.pdf.gz	2.7 MB	Display
Data in XML	8ruw_validation.xml.gz	54.5 KB	Display
Data in CIF	8ruw_validation.cif.gz	70.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ru/8ruw ftp://data.pdbj.org/pub/pdb/validation_reports/ru/8ruw	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

Deposited unit

B: Geranylgeranylglyceryl phosphate synthase

A: Geranylgeranylglyceryl phosphate synthase

C: Geranylgeranylglyceryl phosphate synthase

D: Geranylgeranylglyceryl phosphate synthase

E: Geranylgeranylglyceryl phosphate synthase

F: Geranylgeranylglyceryl phosphate synthase

hetero molecules

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

1

B: Geranylgeranylglyceryl phosphate synthase

C: Geranylgeranylglyceryl phosphate synthase

hetero molecules

defined by author&software
Evidence: gel filtration, 3 dimers in ASU
57.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Geranylgeranylglyceryl phosphate synthase

F: Geranylgeranylglyceryl phosphate synthase

hetero molecules

defined by author&software
57.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Geranylgeranylglyceryl phosphate synthase

E: Geranylgeranylglyceryl phosphate synthase

hetero molecules

defined by author&software
57.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.891, 94.891, 273.791
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	D-420- HOH

#1: Protein	Geranylgeranylglyceryl phosphate synthase / AfGGGPS / GGGP synthase / GGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / ...AfGGGPS / GGGP synthase / GGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / Phosphoglycerol geranylgeranyltransferase Mass: 28471.246 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_0403 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O29844, phosphoglycerol geranylgeranyltransferase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.08 Å³/Da / Density % sol: 40.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M (NH4)2SO4 15% w/v PEG 3350 0.1 M Bis-Tris pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 14, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03322 Å / Relative weight: 1
Reflection	Resolution: 2.48→91.26 Å / Num. obs: 51921 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.196 / R_pim(I) all: 0.055 / R_rim(I) all: 0.203 / Χ²: 0.9 / Net I/σ(I): 9.8 / Num. measured all: 684201
Reflection shell	Resolution: 2.48→2.61 Å / % possible obs: 100 % / Redundancy: 13.6 % / R_merge(I) obs: 1.502 / Num. measured all: 101256 / Num. unique obs: 7472 / CC_1/2: 0.826 / R_pim(I) all: 0.42 / R_rim(I) all: 1.561 / Χ²: 0.83 / Net I/σ(I) obs: 2.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
autoPROC	1.0.5	data processing
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.48→61.07 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2386	2511	4.85 %
R_work	0.2012	-	-
obs	0.203	51821	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.48→61.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10339	0	35	149	10523

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10578
X-RAY DIFFRACTION	f_angle_d	0.58	14423
X-RAY DIFFRACTION	f_dihedral_angle_d	4.545	1464
X-RAY DIFFRACTION	f_chiral_restr	0.046	1676
X-RAY DIFFRACTION	f_plane_restr	0.005	1827

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 (%)
2.48-2.53	0.2913	125	0.2781	2700	X-RAY DIFFRACTION	100
2.53-2.58	0.2861	139	0.2664	2730	X-RAY DIFFRACTION	100
2.58-2.63	0.3248	113	0.2585	2722	X-RAY DIFFRACTION	100
2.63-2.69	0.3028	149	0.2555	2652	X-RAY DIFFRACTION	100
2.69-2.76	0.2516	130	0.2566	2705	X-RAY DIFFRACTION	100
2.76-2.84	0.2623	138	0.2383	2711	X-RAY DIFFRACTION	100
2.84-2.92	0.2552	149	0.236	2704	X-RAY DIFFRACTION	100
2.92-3.01	0.2879	140	0.2304	2687	X-RAY DIFFRACTION	100
3.01-3.12	0.229	135	0.2247	2733	X-RAY DIFFRACTION	100
3.12-3.25	0.2615	124	0.2188	2702	X-RAY DIFFRACTION	100
3.25-3.39	0.2659	146	0.2048	2753	X-RAY DIFFRACTION	100
3.39-3.57	0.256	115	0.193	2748	X-RAY DIFFRACTION	100
3.57-3.8	0.2222	154	0.1787	2735	X-RAY DIFFRACTION	100
3.8-4.09	0.1901	124	0.1669	2747	X-RAY DIFFRACTION	100
4.09-4.5	0.2013	153	0.1597	2772	X-RAY DIFFRACTION	100
4.5-5.15	0.2066	139	0.1624	2771	X-RAY DIFFRACTION	100
5.15-6.49	0.2541	180	0.2046	2771	X-RAY DIFFRACTION	100
6.49-61.07	0.2351	158	0.2057	2967	X-RAY DIFFRACTION	100

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	4.6705	2.8653	0.6853	7.5818	1.7118	3.7973	0.0789	0.4256	0.4746	-0.3952	0.1398	-0.3208	-0.4891	-0.0479	-0.2197	0.3268	0.0108	0.0299	0.3795	0.0921	0.403	12.5602	11.556	-49.0836
2	0.3687	0.5674	0.6462	1.5083	2.247	3.6458	-0.1786	0.036	0.2143	-0.2198	0.1448	0.0958	-0.6555	0.0781	0.0367	0.3612	-0.039	0.0409	0.3135	0.0093	0.3152	16.148	12.2693	-31.1168
3	3.8565	-1.0243	-0.1837	2.5804	-0.2046	5.8255	0.1059	0.2117	-0.0105	-0.2256	0.0653	-0.0028	-0.0355	0.1214	-0.1253	0.2423	-0.0382	0.0166	0.2408	-0.0564	0.1935	17.8448	-4.606	-41.5943
4	5.4659	2.7585	-0.4324	2.6624	0.7713	3.9748	0.1471	-0.4104	-0.0529	0.7494	-0.0082	-0.1439	0.8663	0.0296	-0.18	0.7586	-0.1669	-0.2014	0.7333	0.0421	0.4261	60.4156	41.7533	12.2844
5	1.8368	0.2294	0.7451	0.6672	-1.0415	3.7965	0.3127	-0.2677	0.0007	0.3203	-0.0426	-0.2298	0.1525	0.5196	-0.2036	0.4885	-0.0737	-0.0509	0.5514	-0.0118	0.3672	60.9697	44.4113	-6.8548
6	8.4405	5.0606	3.2783	4.7174	-0.9601	6.3726	0.4471	-1.0629	0.9865	0.6512	-0.4692	0.3524	-0.2821	-1.0826	0.2881	0.6658	0.0045	0.1089	0.5874	-0.1551	0.3887	48.658	60.2054	-0.817
7	1.0756	-0.6013	-0.8093	0.9008	0.5678	5.2489	0.4264	-0.5857	0.1237	0.8401	-0.5638	0.2882	-0.1578	-0.5386	0.0522	0.716	-0.2838	0.0878	0.8837	-0.0497	0.3021	43.5332	46.2662	3.6556
8	1.052	-0.2613	1.0201	0.5758	-0.176	3.8	0.0484	-0.2268	0.1893	0.5274	0.077	0.0025	-0.0705	0.385	0.0915	1.3937	-0.5287	-0.2685	1.0175	-0.3427	-0.0513	53.676	48.2471	21.1502
9	6.8132	2.9761	-0.6659	7.4731	-1.9917	5.4013	-0.0589	0.0365	0.1325	0.3897	0.4773	0.7485	-0.1634	-0.259	-0.3861	0.399	0.0778	0.044	0.3117	0.0324	0.3269	-6.0817	41.9901	-8.4065
10	3.9049	-1.6407	0.7521	2.8321	-0.7573	2.5157	-0.103	0.0537	-0.1423	0.1738	0.2026	0.3115	0.0875	-0.2398	-0.1726	0.2799	-0.0272	0.0451	0.3235	0.0649	0.239	-1.46	36.0795	-24.8649
11	3.0125	-0.0028	-2.7865	1.9998	-0.2974	7.1586	-0.0042	-0.317	0.0708	0.3275	0.0201	-0.0294	-0.3072	0.5172	-0.0583	0.3153	-0.0115	-0.0395	0.2846	0.0034	0.2554	11.1337	42.4314	-13.0315
12	7.7242	-4.3765	3.9498	9.0499	-4.033	6.2773	-0.06	-0.0315	-0.1889	-0.1763	0.4704	0.6058	0.0122	-0.2295	-0.3761	0.3291	-0.1146	0.0356	0.3535	0.0262	0.2149	42.9736	42.5349	-37.3947
13	6.599	-2.5447	1.4558	8.9515	-2.4705	5.6152	-0.2607	-0.4842	0.0936	0.5427	0.254	1.1495	-0.267	-0.824	0.0534	0.3305	-0.0959	0.0295	0.5689	0.0722	0.4574	34.5113	44.5661	-32.1613
14	1.3831	0.0045	0.1906	1.9349	-0.2098	3.3265	0.1341	-0.0383	0.0413	-0.1028	0.0467	-0.0828	-0.0231	-0.0456	-0.1708	0.2792	-0.038	0.0435	0.3057	-0.0166	0.2312	52.3229	45.6224	-27.1767
15	6.6983	-0.9571	-2.0076	5.1785	3.2964	5.451	0.1387	0.3622	-0.3174	-0.3929	0.0254	-0.3835	-0.3238	0.4877	-0.0475	0.4414	0.011	0.0544	0.5111	0.0879	0.3048	11.8362	43.1345	-56.8869
16	3.3067	0.158	1.288	2.3302	-0.1574	3.0143	0.0676	0.0905	-0.1029	-0.2927	-0.0103	0.0656	0.0468	0.0998	-0.0529	0.2842	0.004	0.0029	0.2575	0.0261	0.2008	1.8165	37.5618	-43.207
17	6.3219	-0.9708	-5.2405	6.4868	1.0284	6.6637	-0.249	0.5964	-0.9248	-0.6045	0.0212	0.0744	0.9248	0.0679	-0.0848	0.6656	0.0398	-0.043	0.5747	-0.055	0.4076	0.1819	37.9295	-62.4715
18	6.1179	-0.7701	0.5664	8.9287	-0.2358	2.5776	0.3864	-0.2499	-0.7975	0.2468	-0.45	-0.5275	0.6465	-0.2439	-0.1138	0.4233	-0.0004	0.0089	0.3935	0.0732	0.4103	13.3168	-8.354	2.1473
19	2.372	1.9313	-2.3391	6.4082	1.4964	5.2301	-0.067	0.0053	-0.324	0.3497	-0.0032	-0.2716	0.7684	-0.0831	0.1126	0.457	0.0557	-0.0746	0.3954	-0.0002	0.311	17.5313	-10.1242	-17.0615
20	4.1717	0.8766	-0.3316	2.831	0.5818	4.6032	0.0733	-0.307	-0.0447	0.3329	0.0124	-0.0254	0.0973	0.0482	-0.0878	0.2916	0.0194	-0.0036	0.2682	-0.0319	0.1847	19.2292	7.3014	-5.0485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'E' and (resid 1 through 56 )
2	X-RAY DIFFRACTION	2	chain 'E' and (resid 57 through 126 )
3	X-RAY DIFFRACTION	3	chain 'E' and (resid 127 through 231 )
4	X-RAY DIFFRACTION	4	chain 'F' and (resid 2 through 63 )
5	X-RAY DIFFRACTION	5	chain 'F' and (resid 64 through 126 )
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 127 through 144 )
7	X-RAY DIFFRACTION	7	chain 'F' and (resid 145 through 215 )
8	X-RAY DIFFRACTION	8	chain 'F' and (resid 216 through 230 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 77 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 78 through 144 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 145 through 231 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 1 through 43 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 44 through 77 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 78 through 231 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 2 through 77 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 78 through 207 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 208 through 231 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 0 through 63 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 64 through 118 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 119 through 231 )

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