PDB-7lbj: Crystal structure of octaprenyl diphosphate synthase from Stenotr...

ID or keywords:

Entry

Database: PDB / ID: 7lbj

Title

Crystal structure of octaprenyl diphosphate synthase from Stenotrophomonas maltophilia

Components

Geranyltranstransferase

Keywords

TRANSFERASE / SSGCID / octaprenyl diphosphate synthase / ispB /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease /

LYASE

Function / homology

Function and homology information

(2E,6E)-farnesyl diphosphate synthase /

geranyltranstransferase activity / isoprenoid biosynthetic process
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of octaprenyl diphosphate synthase from Stenotrophomonas maltophilia
Authors: Bolejack, M.J. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jan 8, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7lbj.cif.gz	230.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7lbj.ent.gz	182.5 KB	Display	PDB format
PDBx/mmJSON format	7lbj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lb/7lbj ftp://data.pdbj.org/pub/pdb/validation_reports/lb/7lbj	HTTPS FTP

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Related structure data

Related structure data	3ts7S S: Starting model for refinement
Similar structure data	6sxn-1 5xn6-3 3oac-2 3kro-2 2for-d 6sxl-d 3zl6-d 3krf-2 5xn6-1 4q2g-d 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
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (7)

Deposited unit

A: Geranyltranstransferase

B: Geranyltranstransferase

hetero molecules

64.3 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)	52.060, 60.330, 164.360
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Geranyltranstransferase / / octaprenyl diphosphate synthase Mass: 32062.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: ispA, Smlt3467 / Plasmid: StmaA.01095.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B2FP37, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.01 Å³/Da / Density % sol: 38.88 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: StmaA.01095.a.B1.PW38725 at 18.4 mg/ml was mixed 1:1 with MCSG-1 D3 (313352d3): 0.2 M NaCl, 0.1 M Bis-Tris HCl pH 6.5, 25 (w/v) PEG 3350. Cryo: 15% EG: puck/pin id: yls9-8, aps21idg, 20191212.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.9786 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2019 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9786 Å / Relative weight: 1

Reflection

Resolution: 1.85→29.67 Å / Num. obs: 44553 / % possible obs: 98.8 % / Redundancy: 5.07 % / B_iso Wilson estimate: 19.61 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.049 / R_rim(I) all: 0.054 / Χ²: 1.06 / Net I/σ(I): 21.64 / Num. measured all: 225899

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	2.109	0.26	2.84	6112	3275	2898	0.908	0.331	88.5
1.9-1.95	2.696	0.21	4.31	8381	3192	3109	0.955	0.258	97.4
1.95-2.01	3.275	0.176	6.04	10179	3148	3108	0.968	0.21	98.7
2.01-2.07	4.044	0.152	8.53	12104	2997	2993	0.984	0.175	99.9
2.07-2.14	5.107	0.119	12.7	14913	2921	2920	0.993	0.132	100
2.14-2.21	5.877	0.102	15.99	16891	2875	2874	0.996	0.112	100
2.21-2.29	6.084	0.091	18.31	16689	2744	2743	0.996	0.099	100
2.29-2.39	6.045	0.074	21.41	16038	2656	2653	0.997	0.081	99.9
2.39-2.49	6.032	0.068	23.09	15520	2576	2573	0.997	0.074	99.9
2.49-2.62	5.994	0.06	25.25	14602	2440	2436	0.998	0.066	99.8
2.62-2.76	5.996	0.056	28.07	13911	2323	2320	0.998	0.061	99.9
2.76-2.93	5.961	0.049	31.17	13066	2194	2192	0.998	0.054	99.9
2.93-3.13	5.918	0.046	33.32	12292	2081	2077	0.998	0.05	99.8
3.13-3.38	5.858	0.04	36.32	11434	1955	1952	0.999	0.044	99.8
3.38-3.7	5.826	0.037	38.53	10446	1794	1793	0.999	0.04	99.9
3.7-4.14	5.763	0.035	41.12	9452	1641	1640	0.999	0.038	99.9
4.14-4.78	5.746	0.033	42.83	8407	1466	1463	0.999	0.036	99.8
4.78-5.85	5.759	0.033	40.76	7187	1250	1248	0.999	0.037	99.8
5.85-8.27	5.485	0.03	40.86	5430	991	990	0.999	0.033	99.9
8.27-29.67	4.982	0.032	40.62	2845	596	571	0.999	0.036	95.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19rc4-4035	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ts7

3ts7

Resolution: 1.85→29.67 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1879	2033	4.56 %
R_work	0.1513	42504	-
obs	0.153	44537	98.75 %

Solvent computation

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

Displacement parameters

B_iso max: 81.02 Å² / B_iso mean: 25.4627 Å² / B_iso min: 8.86 Å²

Refinement step

Cycle: final / Resolution: 1.85→29.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4074	0	13	457	4544
B_iso mean	-	-	36.09	31.41	-
Num. residues	-	-	-	-	553

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / 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 (%)
1.85-1.89	0.2872	122	0.2182	2443	2565	87
1.89-1.94	0.2567	138	0.1826	2771	2909	97
1.94-1.99	0.2078	147	0.1701	2749	2896	98
1.99-2.05	0.218	146	0.1606	2794	2940	100
2.05-2.12	0.17	107	0.1421	2864	2971	100
2.12-2.19	0.2011	123	0.1383	2856	2979	100
2.19-2.28	0.1756	142	0.1441	2831	2973	100
2.28-2.38	0.1879	131	0.1445	2836	2967	100
2.38-2.51	0.1992	131	0.1546	2865	2996	100
2.51-2.67	0.2012	139	0.1627	2848	2987	100
2.67-2.87	0.2223	147	0.1543	2879	3026	100
2.87-3.16	0.2	145	0.1554	2857	3002	100
3.16-3.62	0.164	136	0.1476	2903	3039	100
3.62-4.56	0.1553	138	0.1263	2933	3071	100
4.56-29.67	0.1684	141	0.1598	3075	3216	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	4.3408	1.7778	-1.8221	4.3569	-1.1489	3.3161	-0.328	0.3105	-0.3924	-0.1991	0.1351	0.0383	0.5075	-0.2459	0.2105	0.1885	-0.0027	0.0016	0.1583	-0.0686	0.1828	-4.6028	-6.5569	-23.9171
2	4.8219	1.367	-1.8037	2.6098	-0.0763	1.8051	-0.1134	0.3041	-0.3376	-0.1366	0.0313	-0.1437	0.1593	-0.0796	0.0227	0.1507	0.0196	-0.0169	0.1024	-0.0363	0.0959	1.6042	1.7319	-24.2135
3	1.7214	0.2764	-0.4172	1.2133	0.1384	1.0182	-0.0384	0.0253	-0.1437	0.0534	0.0071	-0.18	0.0865	0.1235	0.0238	0.1209	0.0186	-0.0069	0.0913	-0.0048	0.1144	6.6133	9.0915	-19.7575
4	1.4196	0.0561	0.2941	1.9033	-0.3548	2.2882	-0.0112	-0.1258	-0.0091	0.2691	-0.0715	-0.1922	-0.1061	0.151	0.0964	0.1525	-0.0018	-0.0086	0.101	-0.0004	0.1042	1.5084	10.2017	-5.9239
5	3.0206	-0.3651	1.2546	2.0265	-0.3451	3.5675	-0.0814	-0.0719	-0.3321	0.1132	0.127	-0.1357	0.1659	0.1925	-0.0122	0.1482	0.0151	0.035	0.1041	-0.0056	0.1419	-1.5534	-1.021	0.5995
6	6.0993	0.2236	2.6706	3.0348	0.6167	5.7477	0.0037	0.086	-0.6464	0.0434	0.0114	-0.0114	0.4799	0.1672	-0.108	0.2577	-0.0192	0.0454	0.1218	-0.0033	0.2445	-10.1735	-6.9593	-8.078
7	1.6889	-0.7667	0.6225	2.0976	-1.2265	2.2616	0.0989	0.0172	0.1678	-0.0284	-0.0772	-0.0251	-0.2978	-0.0563	-0	0.1561	0.0093	0.0136	0.0924	-0.0094	0.1117	5.9283	33.6618	-19.2725
8	3.7959	0.5684	2.2209	0.9554	0.0539	2.5095	-0.0213	-0.0065	0.1215	-0.0293	-0.0242	0.0062	-0.0968	0.0673	0.0397	0.1176	0.0086	0.0199	0.0612	-0.0071	0.1037	9.568	23.0647	-19.129
9	0.3527	0.8037	-0.6295	2.8039	-0.2794	2.8158	0.1989	0.2881	-0.0568	-0.4583	-0.1955	-0.463	0.0584	0.2432	-0.0225	0.2066	0.0436	0.055	0.177	0.005	0.1476	12.0683	22.9393	-34.6488
10	3.337	0.4892	-0.56	4.3099	-0.8876	4.0842	-0.1089	0.1629	-0.1262	-0.2375	-0.0813	-0.7219	-0.1269	0.4645	0.0344	0.2466	0.0651	0.0508	0.2544	0.0593	0.2141	15.8536	34.1119	-40.4077
11	3.1366	-0.4203	-0.2741	4.9026	-1.0559	4.5133	0.3177	0.2658	0.3048	0.3998	0.0102	-0.0743	-0.7323	0.0132	-0.0661	0.4831	0.0748	0.0812	0.187	0.0609	0.1907	7.1203	42.8813	-36.9634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 21 )	A	0 - 21
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 66 )	A	22 - 66
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 67 through 146 )	A	67 - 146
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 147 through 197 )	A	147 - 197
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 198 through 269 )	A	198 - 269
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 270 through 292 )	A	270 - 292
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 84 )	B	0 - 84
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 85 through 146 )	B	85 - 146
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 147 through 197 )	B	147 - 197
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 198 through 269 )	B	198 - 269
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 270 through 292 )	B	270 - 292

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