PDB-5nf1: crystal structure of variants

ID or keywords:

Entry

Database: PDB / ID: 5nf1

Title

crystal structure of variants

Components

Geranylgeranylglyceryl phosphate synthase

Keywords

TRANSFERASE / Methanobacterium thermoautotrophicum

Function / homology

Function and homology information

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

Biological species

Methanothermobacter thermautotrophicus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.697 Å

Authors

Linde, M. / Rajendran, C. / Babinger, P. / Sterner, R.

Citation

Journal: To Be Published
Title: crystal structure of variants
Authors: Linde, M. / Rajendran, C. / Babinger, P. / Sterner, R.

History

Deposition	Mar 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5nf1.cif.gz	502.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5nf1.ent.gz	421.5 KB	Display	PDB format
PDBx/mmJSON format	5nf1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5nf1_validation.pdf.gz	487.8 KB	Display	wwPDB validaton report
Full document	5nf1_full_validation.pdf.gz	525.8 KB	Display
Data in XML	5nf1_validation.xml.gz	50.4 KB	Display
Data in CIF	5nf1_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nf/5nf1 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/5nf1	HTTPS FTP

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Related structure data

Similar structure data	5ndy-d 6qq2-1 5nez-d 4mm1-d 6qpv-2 4ax3-4 4ax3-3 6f1q-1 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

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

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	83.198, 62.783, 136.259
Angle α, β, γ (deg.)	90.00, 96.35, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Geranylgeranylglyceryl phosphate synthase / MtGGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / Phosphoglycerol geranylgeranyltransferase Mass: 27506.270 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea) Gene: MTH_552 / Production host: Escherichia coli (E. coli) References: UniProt: O26652, phosphoglycerol geranylgeranyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Geranylgeranylglyceryl phosphate synthase / MtGGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / Phosphoglycerol geranylgeranyltransferase

Mass: 27506.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Gene: MTH_552 / Production host:

Escherichia coli (E. coli)
References: UniProt: O26652, phosphoglycerol geranylgeranyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.61 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / Details: PEG Tris cl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.697→47.962 Å / Num. obs: 35020 / % possible obs: 97.52 % / Redundancy: 3.3 % / R_pim(I) all: 0.05656 / Net I/σ(I): 10.18
Reflection shell	R_pim(I) all: 0.3459 / R_rim(I) all: 0.6238

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.697→47.962 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3212	1751	5 %
R_work	0.2317	-	-
obs	0.2361	35020	89.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.697→47.962 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9932	0	0	43	9975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10090
X-RAY DIFFRACTION	f_angle_d	1.072	13722
X-RAY DIFFRACTION	f_dihedral_angle_d	5.732	6038
X-RAY DIFFRACTION	f_chiral_restr	0.058	1620
X-RAY DIFFRACTION	f_plane_restr	0.007	1807

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 (%)
2.6972-2.7701	0.56	14	0.3819	265	X-RAY DIFFRACTION	9
2.7701-2.8516	0.4126	127	0.314	2416	X-RAY DIFFRACTION	85
2.8516-2.9437	0.3683	149	0.2944	2833	X-RAY DIFFRACTION	100
2.9437-3.0489	0.3801	146	0.2776	2782	X-RAY DIFFRACTION	100
3.0489-3.1709	0.3335	150	0.2768	2848	X-RAY DIFFRACTION	100
3.1709-3.3152	0.3541	149	0.2715	2815	X-RAY DIFFRACTION	100
3.3152-3.4899	0.3387	149	0.2527	2843	X-RAY DIFFRACTION	99
3.4899-3.7085	0.3515	146	0.2355	2773	X-RAY DIFFRACTION	99
3.7085-3.9947	0.2959	145	0.2185	2749	X-RAY DIFFRACTION	97
3.9947-4.3965	0.2972	144	0.2121	2729	X-RAY DIFFRACTION	96
4.3965-5.0321	0.283	144	0.1862	2748	X-RAY DIFFRACTION	97
5.0321-6.3376	0.3482	148	0.2437	2804	X-RAY DIFFRACTION	97
6.3376-47.9691	0.2865	140	0.204	2664	X-RAY DIFFRACTION	90

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	3.5662	-0.1749	-0.504	2.8885	0.1612	1.9549	0.0248	0.2332	0.0081	0.2949	-0.0649	0.7117	0.2553	-0.391	0.0333	0.3999	-0.0513	0.0952	0.3528	-0.0117	0.522	79.1668	-51.5226	62.3187
2	0.9481	0.2325	-0.1967	1.492	0.1081	1.9148	-0.0714	-0.0062	-0.0537	0.0598	0.0151	-0.1098	0.1939	-0.0346	0.0539	0.2837	-0.0119	0.0251	0.2286	-0.0511	0.3461	94.164	-53.7279	55.6802
3	1.4977	-0.4895	0.1993	2.8447	0.2934	2.049	0.2551	0.4617	0.3882	-0.9258	-0.0642	0.2548	0.4982	0.4371	-0.0785	1.3082	0.1006	-0.1818	0.54	0.0231	0.3502	86.934	-53.8941	5.6864
4	1.3488	-0.1749	0.7847	3.3471	0.3737	2.6676	0.2331	0.0645	-0.2392	-0.3278	0.0297	0.049	0.7122	0.0691	-0.1948	0.5657	-0.0097	-0.095	0.2877	0.0119	0.3464	84.5453	-53.7608	24.0291
5	2.335	0.2966	-0.3543	2.8123	-0.3909	1.8929	0.0836	0.0948	-0.5964	0.3189	-0.2228	-0.744	-0.1921	0.3999	0.1828	0.5399	-0.0385	-0.1935	0.5265	-0.0013	0.7711	118.0794	-26.6745	62.1104
6	0.4702	-0.2885	0.4038	2.907	0.7336	1.8351	-0.2097	0.063	0.1081	0.0023	0.0353	-0.307	-0.4143	0.2295	0.1461	0.2857	-0.065	-0.0213	0.3164	0.0215	0.3998	103.3505	-25.7555	54.4884
7	1.8159	0.6139	0.3894	3.3606	0.7331	3.0232	0.188	-0.0283	-0.166	0.8112	-0.428	0.534	0.0848	0.0453	0.2038	0.6586	0.0899	0.0413	0.5704	-0.0317	0.697	64.515	-28.1829	33.0199
8	1.9917	-0.619	-1.7125	1.859	0.6423	1.4614	-0.4595	-1.0974	0.3057	0.823	0.6311	0.0761	0.2327	-0.0892	-0.1739	0.737	0.0391	0.1914	0.7334	-0.0209	0.5721	65.9174	-31.4962	43.9984
9	1.4044	-0.6565	-0.4378	2.876	0.1599	2.0289	-0.0198	0.0566	0.1767	0.2382	0.0056	0.2414	-0.2887	0.1605	-0.0147	0.5547	-0.086	-0.059	0.3429	0.0406	0.3739	79.8521	-29.2577	29.8064
10	0.8674	1.4848	0.1712	2.4151	-0.4251	3.4284	0.2632	0.1223	-0.0411	0.9142	-0.8328	-1.0954	-0.2317	0.7106	0.3249	0.3912	0.0362	-0.0499	0.9577	0.1961	0.7276	131.6013	-49.48	39.5534
11	1.7323	-0.599	1.4361	1.9246	-1.0015	1.3052	0.0433	0.2214	-0.3234	-0.2194	0.0506	-0.0706	0.25	0.2202	-0.0336	0.4958	-0.0277	0.1435	0.6726	-0.0239	0.4614	117.8563	-53.0272	29.7658
12	3.8678	0.3269	0.9159	1.5601	0.5501	2.5392	-0.6344	0.7327	0.4606	-1.2013	-0.0651	-0.044	-0.5563	-0.1331	0.4594	0.9335	-0.1207	-0.0208	1.0069	0.1228	0.5557	107.9797	-26.7475	3.9591
13	2.6733	0.4817	0.8668	1.2117	-0.9527	1.9221	-0.1338	0.3388	0.4837	0.0311	-0.2175	-0.0615	-0.5805	0.4181	0.2683	0.5121	-0.166	-0.0052	0.7096	0.1096	0.4874	110.6632	-27.501	19.5167

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 91 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 92 through 246 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 4 through 91 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 92 through 224 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 2 through 91 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 92 through 246 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 2 through 30 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 31 through 91 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 92 through 225 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 2 through 91 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 92 through 246 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 3 through 71 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 72 through 246 )

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