PDB-7my7: Se-CrtE N-term His-tag structure

ID or keywords:

Entry

Database: PDB / ID: 7my7

Title

Se-CrtE N-term His-tag structure

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.36 Å

Authors

Peat, T.S. / Newman, J.

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	Jun 1, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 24, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	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 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7my7.cif.gz	207.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7my7.ent.gz		Display	PDB format
PDBx/mmJSON format	7my7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7my7_validation.pdf.gz	469.5 KB	Display	wwPDB validaton report
Full document	7my7_full_validation.pdf.gz	492 KB	Display
Data in XML	7my7_validation.xml.gz	34.6 KB	Display
Data in CIF	7my7_validation.cif.gz	47.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/my/7my7 ftp://data.pdbj.org/pub/pdb/validation_reports/my/7my7	HTTPS FTP

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Related structure data

Related structure data	7mxzC 7my0C 7my1C 7my6SC 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

AAA: Farnesyl-diphosphate synthase

BBB: Farnesyl-diphosphate synthase

CCC: Farnesyl-diphosphate synthase

DDD: Farnesyl-diphosphate synthase

139 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Farnesyl-diphosphate synthase

BBB: Farnesyl-diphosphate synthase

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

2

CCC: Farnesyl-diphosphate synthase

DDD: Farnesyl-diphosphate synthase

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

Unit cell

Length a, b, c (Å)	155.512, 56.443, 144.812
Angle α, β, γ (deg.)	90.000, 100.377, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PHE	PHE	ALA	ALA	AAA	A	9 - 298	30 - 319
2	1	1	PHE	PHE	ALA	ALA	BBB	B	9 - 298	30 - 319
3	2	2	ASP	ASP	GLN	GLN	AAA	A	10 - 225	31 - 246
4	2	2	ASP	ASP	GLN	GLN	CCC	C	10 - 225	31 - 246
5	3	3	LYS	LYS	THR	THR	AAA	A	12 - 297	33 - 318
6	3	3	LYS	LYS	THR	THR	DDD	D	12 - 297	33 - 318
7	4	4	ASP	ASP	GLN	GLN	BBB	B	10 - 225	31 - 246
8	4	4	ASP	ASP	GLN	GLN	CCC	C	10 - 225	31 - 246
9	5	5	LYS	LYS	THR	THR	BBB	B	12 - 297	33 - 318
10	5	5	LYS	LYS	THR	THR	DDD	D	12 - 297	33 - 318
11	6	6	LYS	LYS	GLN	GLN	CCC	C	12 - 225	33 - 246
12	6	6	LYS	LYS	GLN	GLN	DDD	D	12 - 225	33 - 246

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Farnesyl-diphosphate synthase Mass: 34710.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (strain 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
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Farnesyl-diphosphate synthase

Mass: 34710.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Synechococcus elongatus (strain 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

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.25 Å³/Da / Density % sol: 45.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 200 nL of protein at 10 mg/mL was added to 200 nL of reservoir containing 22.6% (w/v) polyacrylic acid 2100, 1.0% ethylammonium nitrate and 10% (v/v) DL-malate-MES-tris buffer at pH 7.0

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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: Nov 14, 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: 2.36→48.65 Å / Num. obs: 51379 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.144 / R_pim(I) all: 0.083 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.36→2.43 Å / R_merge(I) obs: 1.578 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4201 / CC_1/2: 0.553 / R_pim(I) all: 0.659 / % possible all: 95.1

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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: 7MY6

7my6

Resolution: 2.36→48.65 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.934 / SU B: 9.309 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.336 / ESU R Free: 0.234
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2469	2566	4.994 %
R_work	0.2184	48811	-
all	0.22	-	-
obs	-	51377	99.525 %

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: 65.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.58 Å²	0 Å²	2.614 Å²
2-	-	-1.411 Å²	0 Å²
3-	-	-	0.969 Å²

Refinement step

Cycle: LAST / Resolution: 2.36→48.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7489	0	0	75	7564

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	7623
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7211
X-RAY DIFFRACTION	r_angle_refined_deg	1.371	1.633	10403
X-RAY DIFFRACTION	r_angle_other_deg	1.347	1.572	16522
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.05	5	1017
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.596	22.351	353
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.348	15	1159
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.042	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1074
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8775
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1581
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1644
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	5959
X-RAY DIFFRACTION	r_nbtor_refined	0.15	0.2	3807
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3296
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	105
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.386	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.339	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.162	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	5.065	7.029	4089
X-RAY DIFFRACTION	r_mcbond_other	5.055	7.029	4088
X-RAY DIFFRACTION	r_mcangle_it	7.273	10.515	5099
X-RAY DIFFRACTION	r_mcangle_other	7.272	10.516	5100
X-RAY DIFFRACTION	r_scbond_it	5.485	7.36	3534
X-RAY DIFFRACTION	r_scbond_other	5.48	7.36	3534
X-RAY DIFFRACTION	r_scangle_it	8.257	10.88	5304
X-RAY DIFFRACTION	r_scangle_other	8.258	10.88	5304
X-RAY DIFFRACTION	r_lrange_it	11.708	132.464	32400
X-RAY DIFFRACTION	r_lrange_other	11.712	132.514	32372
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.082	0.05	8679
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	6449
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.088	0.05	7746
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.065	0.05	6358
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.08	0.05	7716
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.061	0.05	6097

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.08193	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.08193	0.05008
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.06376	0.05008
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.06376	0.05008
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.08768	0.05008
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.08768	0.05008
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.06485	0.05008
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.06485	0.05008
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.08006	0.05008
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.08006	0.05008
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.06105	0.05008
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.06105	0.05008

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 (%)
2.36-2.417	0.337	150	0.325	3382	X-RAY DIFFRACTION	94.0612
2.417-2.483	0.344	187	0.313	3505	X-RAY DIFFRACTION	100
2.483-2.555	0.349	171	0.3	3445	X-RAY DIFFRACTION	100
2.555-2.634	0.297	161	0.281	3291	X-RAY DIFFRACTION	100
2.634-2.72	0.279	154	0.259	3232	X-RAY DIFFRACTION	100
2.72-2.815	0.301	182	0.244	3105	X-RAY DIFFRACTION	100
2.815-2.922	0.263	147	0.23	2994	X-RAY DIFFRACTION	99.9364
2.922-3.041	0.269	142	0.213	2922	X-RAY DIFFRACTION	100
3.041-3.176	0.24	146	0.207	2781	X-RAY DIFFRACTION	100
3.176-3.331	0.247	150	0.206	2660	X-RAY DIFFRACTION	100
3.331-3.511	0.249	149	0.215	2511	X-RAY DIFFRACTION	100
3.511-3.724	0.24	133	0.2	2408	X-RAY DIFFRACTION	100
3.724-3.981	0.218	113	0.183	2258	X-RAY DIFFRACTION	100
3.981-4.3	0.187	133	0.17	2073	X-RAY DIFFRACTION	100
4.3-4.71	0.199	104	0.151	1956	X-RAY DIFFRACTION	100
4.71-5.265	0.192	99	0.18	1744	X-RAY DIFFRACTION	100
5.265-6.078	0.318	79	0.236	1574	X-RAY DIFFRACTION	100
6.078-7.44	0.329	82	0.284	1324	X-RAY DIFFRACTION	100
7.44-10.508	0.207	52	0.221	1052	X-RAY DIFFRACTION	99.8192
10.508-48.65	0.232	32	0.263	595	X-RAY DIFFRACTION	97.2093

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