PDB-7my6: Se-CrtE C-term His-tag with IPP added

ID or keywords:

Entry

Database: PDB / ID: 7my6

Title

Se-CrtE C-term His-tag with IPP added

Components

Farnesyl-diphosphate synthase

Keywords

TRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids

Function / homology

Function and homology information

dimethylallyltranstransferase / terpenoid biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.02 Å

Authors

Peat, T.S. / Newman, J.

Funding support

1items

Citation

Journal: Febs J. / Year: 2022
Title: Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase.
Authors: Satta, A. / Esquirol, L. / Ebert, B.E. / Newman, J. / Peat, T.S. / Plan, M. / Schenk, G. / Vickers, C.E.

History

Deposition	May 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 24, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7my6.cif.gz	134.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7my6.ent.gz	98.8 KB	Display	PDB format
PDBx/mmJSON format	7my6.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/my/7my6 ftp://data.pdbj.org/pub/pdb/validation_reports/my/7my6	HTTPS FTP

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Related structure data

Related structure data	7mxzSC 7my0C 7my1C 7my7C S: Starting model for refinement C: citing same article (ref.)
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 (7)

Deposited unit

A: Farnesyl-diphosphate synthase

B: Farnesyl-diphosphate synthase

hetero molecules

68.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	45.423, 144.627, 48.066
Angle α, β, γ (deg.)	90.000, 95.249, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Farnesyl-diphosphate synthase Mass: 33592.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 / FACHB-805 / Gene: Synpcc7942_0776 / Production host: Escherichia coli (E. coli) References: UniProt: Q31Q61, (2E,6E)-farnesyl diphosphate synthase

#1: Protein

Farnesyl-diphosphate synthase

Mass: 33592.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: Synpcc7942_0776 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q31Q61, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 7 types, 264 molecules

#2: Chemical	ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₂O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 200 nL of protein at 10 mg/mL was added to 200 nL of reservoir consisting of 90 mM CHES pH 9.5, 180 mM magnesium sulfate, 100 mM trisodium citrate, 22.5% (w/v) PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.94→48.21 Å / Num. obs: 45579 / % possible obs: 99.9 % / Redundancy: 10 % / CC_1/2: 0.986 / R_merge(I) obs: 0.345 / R_pim(I) all: 0.113 / Net I/σ(I): 5.7
Reflection shell	Resolution: 1.94→1.99 Å / Redundancy: 9.7 % / R_merge(I) obs: 2.327 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3076 / CC_1/2: 0.392 / R_pim(I) all: 0.781

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7mxz

7mxz

Resolution: 2.02→45.482 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.932 / WR_factor R_free: 0.189 / WR_factor R_work: 0.163 / SU B: 5.122 / SU ML: 0.134 / Average fsc free: 0.9021 / Average fsc work: 0.9103 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2088	2053	5.092 %
R_work	0.1804	38268	-
all	0.182	-	-
obs	-	40321	99.866 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 22.581 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.512 Å²	-0 Å²	-0.154 Å²
2-	-	-1.333 Å²	-0 Å²
3-	-	-	1.842 Å²

Refinement step

Cycle: LAST / Resolution: 2.02→45.482 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4347	0	63	248	4658

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	4503
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	4376
X-RAY DIFFRACTION	r_angle_refined_deg	1.407	1.635	6115
X-RAY DIFFRACTION	r_angle_other_deg	1.393	1.575	10058
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.161	5	577
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.028	21.786	224
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.13	10	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.325	15	749
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.68	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	610
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5067
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	949
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1130
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	4081
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	2272
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1881
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	249
X-RAY DIFFRACTION	r_metal_ion_refined	0.167	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.092	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.153	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.162	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	1.662	2.184	2308
X-RAY DIFFRACTION	r_mcbond_other	1.662	2.182	2307
X-RAY DIFFRACTION	r_mcangle_it	2.639	3.257	2885
X-RAY DIFFRACTION	r_mcangle_other	2.639	3.258	2886
X-RAY DIFFRACTION	r_scbond_it	2.62	2.556	2195
X-RAY DIFFRACTION	r_scbond_other	2.59	2.539	2180
X-RAY DIFFRACTION	r_scangle_it	4.122	3.694	3230
X-RAY DIFFRACTION	r_scangle_other	4.105	3.666	3207
X-RAY DIFFRACTION	r_lrange_it	6.738	41.143	19679
X-RAY DIFFRACTION	r_lrange_other	6.685	41.098	19506

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 (%)
2.02-2.072	0.277	159	0.278	2803	X-RAY DIFFRACTION	100
2.072-2.129	0.293	134	0.238	2755	X-RAY DIFFRACTION	99.9308
2.129-2.191	0.225	145	0.23	2699	X-RAY DIFFRACTION	99.9649
2.191-2.258	0.221	133	0.216	2588	X-RAY DIFFRACTION	99.9633
2.258-2.332	0.233	151	0.199	2487	X-RAY DIFFRACTION	100
2.332-2.413	0.233	135	0.19	2456	X-RAY DIFFRACTION	99.9229
2.413-2.504	0.199	127	0.18	2352	X-RAY DIFFRACTION	100
2.504-2.606	0.251	118	0.177	2220	X-RAY DIFFRACTION	99.9572
2.606-2.722	0.195	136	0.174	2193	X-RAY DIFFRACTION	100
2.722-2.854	0.237	124	0.176	2079	X-RAY DIFFRACTION	99.9546
2.854-3.008	0.215	107	0.166	1987	X-RAY DIFFRACTION	99.9523
3.008-3.189	0.199	80	0.164	1852	X-RAY DIFFRACTION	99.3316
3.189-3.408	0.195	64	0.168	1787	X-RAY DIFFRACTION	100
3.408-3.68	0.188	70	0.164	1666	X-RAY DIFFRACTION	99.9424
3.68-4.028	0.212	82	0.155	1512	X-RAY DIFFRACTION	99.9373
4.028-4.499	0.15	87	0.148	1357	X-RAY DIFFRACTION	100
4.499-5.187	0.171	77	0.148	1192	X-RAY DIFFRACTION	99.9213
5.187-6.332	0.208	57	0.212	1030	X-RAY DIFFRACTION	99.9081
6.332-8.869	0.173	51	0.146	783	X-RAY DIFFRACTION	99.2857
8.869-45.482	0.162	16	0.163	470	X-RAY DIFFRACTION	98.5801

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