PDB-4mm1: GGGPS from Methanothermobacter thermautotrophicus

ID or keywords:

Entry

Database: PDB / ID: 4mm1

Title

GGGPS from Methanothermobacter thermautotrophicus

Components

Geranylgeranylglyceryl phosphate synthase

Keywords

TRANSFERASE / GGGPS

Function / homology

Function and homology information

phosphoglycerol geranylgeranyltransferase /

phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / polyprenyltransferase activity / magnesium ion binding /

cytoplasm
Similarity search - Function

Biological species

Methanothermobacter thermautotrophicus str. Delta H (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8004 Å

Authors

Rajendran, C. / Peterhoff, D. / Beer, B. / Kumpula, E.P. / Kapetaniou, E. / Guldan, H. / Wierenga, R.K. / Sterner, R. / Babinger, P.

Citation

Journal: Mol.Microbiol. / Year: 2014
Title: A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization.
Authors: Peterhoff, D. / Beer, B. / Rajendran, C. / Kumpula, E.P. / Kapetaniou, E. / Guldan, H. / Wierenga, R.K. / Sterner, R. / Babinger, P.

History

Deposition	Sep 7, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 25, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Mar 13, 2024	Group: Source and taxonomy / Category: entity_src_nat

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mm1.cif.gz	705.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4mm1.ent.gz	603.5 KB	Display	PDB format
PDBx/mmJSON format	4mm1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mm/4mm1 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mm1	HTTPS FTP

-
Related structure data

Related structure data	4jejC 4naeC 4nafC C: citing same article (ref.)
Similar structure data	5nf1-d 6qpv-2 8xim-d 5kaj-4 5k0n-d 4i6v-d 6qq2-1 5kaj-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4jejC

4naeC

4nafC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Geranylgeranylglyceryl phosphate synthase

B: Geranylgeranylglyceryl phosphate synthase

C: Geranylgeranylglyceryl phosphate synthase

D: Geranylgeranylglyceryl phosphate synthase

E: Geranylgeranylglyceryl phosphate synthase

F: Geranylgeranylglyceryl phosphate synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

A: Geranylgeranylglyceryl phosphate synthase

B: Geranylgeranylglyceryl phosphate synthase

hetero molecules

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

3

C: Geranylgeranylglyceryl phosphate synthase

E: Geranylgeranylglyceryl phosphate synthase

hetero molecules

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

4

D: Geranylgeranylglyceryl phosphate synthase

F: Geranylgeranylglyceryl phosphate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	143.675, 148.756, 91.503
Angle α, β, γ (deg.)	90.00, 109.50, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Geranylgeranylglyceryl phosphate synthase / GGGP synthase / GGGPS / MtGGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / ...GGGP synthase / GGGPS / MtGGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / Phosphoglycerol geranylgeranyltransferase Mass: 26792.518 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_552 / Production host: Escherichia coli (E. coli) References: UniProt: O26652, phosphoglycerol geranylgeranyltransferase
#2: Chemical	ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE Mass: 172.074 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₉O₆P
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.62 %

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→46.563 Å / Num. all: 74185 / Num. obs: 42401 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.3

-
Processing

Software

Name	Version	Classification
PHENIX		model building
PHENIX	(phenix.refine: dev_1417)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8004→46.563 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8099 / SU ML: 0.42 / σ(F): 0.37 / Phase error: 28.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2708	2120	5 %
R_work	0.2004	40256	-
obs	0.204	42376	95.05 %

Solvent computation

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

Displacement parameters

B_iso max: 165.88 Å² / B_iso mean: 44.4005 Å² / B_iso min: 11.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.8004→46.563 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9873	0	120	68	10061

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10267
X-RAY DIFFRACTION	f_angle_d	1.021	13913
X-RAY DIFFRACTION	f_chiral_restr	0.04	1607
X-RAY DIFFRACTION	f_plane_restr	0.004	1800
X-RAY DIFFRACTION	f_dihedral_angle_d	14.209	3700

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8004-2.8655	0.3055	141	0.2458	2680	2821	95
2.8655-2.9372	0.37	147	0.242	2803	2950	100
2.9372-3.0166	0.3166	147	0.237	2798	2945	100
3.0166-3.1053	0.322	148	0.2373	2796	2944	100
3.1053-3.2055	0.3212	147	0.2364	2793	2940	99
3.2055-3.3201	0.3311	146	0.2351	2778	2924	98
3.3201-3.4529	0.2929	145	0.2154	2764	2909	98
3.4529-3.61	0.2811	143	0.2047	2717	2860	97
3.61-3.8003	0.2612	144	0.1839	2730	2874	96
3.8003-4.0383	0.2299	141	0.1793	2680	2821	95
4.0383-4.3498	0.2819	141	0.178	2677	2818	94
4.3498-4.7872	0.202	136	0.1551	2569	2705	91
4.7872-5.479	0.23	130	0.1646	2477	2607	88
5.479-6.8993	0.2667	131	0.2195	2479	2610	87
6.8993-46.5689	0.2485	133	0.2027	2515	2648	87

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	1.2585	0.9527	0.4895	1.5707	0.0489	1.1791	0.1663	-0.2091	-0.3717	0.1051	-0.0827	-0.1361	0.2718	-0.0087	-0.0791	0.2951	-0.0377	0.0479	0.238	0.054	0.3071	26.9402	19.5305	50.075
2	1.6059	-0.4235	0.8352	3.3596	1.2801	2.0491	0.099	-0.1232	-0.3021	-0.3809	0.022	-0.3841	-0.2527	0.2263	-0.0477	0.2846	-0.0801	0.0485	0.28	0.0258	0.3822	27.9446	16.6709	41.4752
3	0.6267	-0.0288	0.0053	0.7684	-0.314	1.2955	0.0166	-0.1948	-0.1198	0.0218	-0.0856	0.0277	0.0572	-0.1408	0.0244	0.1685	-0.0304	0.0284	0.2189	0.0213	0.2591	28.2801	34.1681	43.7023
4	0.8586	-0.1676	-0.0981	1.7585	-0.1656	2.1006	-0.625	-0.1413	-0.2555	-0.315	0.1092	-0.1476	0.0092	-0.4725	0.2851	0.3113	0.005	-0.0206	0.4104	0.0271	0.6702	-2.4997	52.7984	35.5252
5	1.3558	-0.6691	-0.5191	1.3117	0.1302	0.243	-0.0071	-0.1585	0.4854	-0.0419	0.092	0.3247	-0.2612	-0.2071	0.0664	0.3211	0.101	0.0295	0.3922	0.0041	0.5502	6.8099	55.7158	37.7873
6	0.9644	-0.3005	-0.1771	1.0261	-0.1972	0.3339	0.0392	0.144	0.0388	-0.0687	-0.0604	0.3117	-0.0357	-0.1783	-0.0168	0.2043	-0.0077	-0.0783	0.3088	0.0256	0.353	10.8125	43.1956	28.4848
7	0.9272	0.256	0.1996	0.5595	0.1139	0.6021	0.1112	0.0033	-0.26	0.0073	-0.097	0.2913	0.0883	-0.1482	0.3316	0.2319	-0.1336	-0.1429	0.5874	0.0041	0.5336	0.8222	37.1233	27.7394
8	0.9443	-0.9444	0.007	2.0771	-0.7692	0.514	0.0099	0.1621	0.0039	-0.3928	0.1581	0.5141	0.1518	-0.3606	-0.0897	0.3356	-0.0656	-0.2368	0.4497	0.0064	0.9263	-6.1288	41.9735	25.195
9	1.3354	0.1931	0.7023	2.3931	-0.4693	1.53	-0.1	0.4706	0.0719	-0.2995	0.0418	0.0961	0.0023	0.0546	0.1358	0.3383	0.031	0.1241	0.4065	0.0289	0.2679	60.7329	41.9535	5.7311
10	1.3253	0.0006	0.1102	0.9958	0.2918	0.7394	0.0707	0.0103	-0.0076	-0.132	0.1109	-0.0576	-0.0015	0.2371	-0.1251	0.3	0.0271	0.0139	0.2437	-0.0303	0.1443	51.3241	37.395	16.7152
11	1.6047	-0.4531	0.3878	1.2192	-0.2317	1.4851	-0.093	-0.2638	0.2672	0.137	0.0181	-0.071	-0.106	0.0635	0.2239	0.2264	0.0091	0.0591	0.2746	-0.0913	0.4053	33.5128	78.619	38.9334
12	2.2501	0.3102	0.1608	2.5059	0.4837	2.0264	0.0817	0.1592	-0.4714	0.1767	-0.2232	0.1972	0.4217	0.1217	-0.0402	0.3376	0.0452	0.041	0.2954	-0.1347	0.4781	28.1575	69.5977	40.7735
13	1.0912	-0.1621	-0.3008	1.6643	0.6321	1.2937	0.3552	-0.0496	0.188	0.4787	-0.1615	0.2386	-0.0044	-0.1393	-0.1785	0.3584	0.0255	0.0924	0.3649	-0.0675	0.4745	22.1085	73.3639	39.9244
14	0.8878	0.6179	-0.1651	1.0422	0.257	1.0364	-0.0279	-0.229	0.1822	0.0159	0.0217	-0.0236	0.0235	0.0431	0.1104	0.2211	0.0385	0.0315	0.1909	-0.0046	0.2562	34.6053	62.1826	28.4537
15	2.0336	-0.2089	-0.2287	1.5982	0.0899	2.3159	-0.2566	0.17	-0.1561	-0.0108	0.1416	-0.2597	0.0832	0.2087	0.0246	0.2467	0.0088	0.0316	0.2464	-0.0258	0.3698	46.4223	69.6542	33.1344
16	1.9432	0.4325	-0.113	1.5538	-0.6057	2.6672	-0.0857	0.1048	-0.3275	-0.1761	0.3213	-0.1123	0.3774	-0.3099	-0.2421	0.4788	-0.0404	0.017	0.3558	-0.077	0.454	24.2649	11.786	9.8764
17	1.1175	-0.0058	-0.2286	0.8831	0.4379	1.1533	0.0366	0.2646	-0.0781	-0.3009	-0.123	0.2768	0.0683	-0.0008	0.027	0.3861	-0.0241	-0.0634	0.2672	-0.0548	0.2504	27.6427	27.8036	7.729
18	0.6395	-0.8387	-0.0173	1.1956	0.1534	0.8256	-0.0137	0.1264	0.3346	-0.4674	0.1067	-0.1474	-0.4387	0.0332	0.13	0.8369	0.0765	0.0506	0.3998	0.1416	0.3397	32.6302	70.4067	-5.5648
19	0.3863	-0.0049	0.0134	1.4196	-0.1749	1.1101	-0.0595	0.0104	0.0717	-0.3315	0.0027	-0.1292	-0.0772	-0.141	0.0579	0.3582	0.0336	-0.0363	0.2586	0.0497	0.278	28.9482	60.1352	9.4727
20	1.5549	0.7485	-0.2647	1.4741	1.1419	1.501	-0.1872	0.3517	0.5702	-0.5065	-0.2149	0.5266	0.2382	0.1065	0.0612	0.5438	0.1338	-0.1489	0.4092	0.1124	0.4673	16.5257	67.3421	3.1809

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 43 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 79 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 246 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 57 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 58 through 103 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 104 through 187 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 188 through 207 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 208 through 225 )	B
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 71 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 72 through 248 )	C
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 44 )	D
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 45 through 58 )	D
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 59 through 91 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 92 through 184 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 185 through 225 )	D
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 1 through 71 )	E
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 72 through 225 )	E
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 2 through 74 )	F
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 75 through 184 )	F
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 185 through 224 )	F

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi