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- PDB-8x35: Neryl diphosphate synthase from Solanum lycopersicum complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8x35
TitleNeryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)
ComponentsNeryl diphosphate synthase 1
KeywordsTRANSFERASE / cis-prenyltransferase
Function / homology
Function and homology information


dimethylallylcistransferase / dimethylallylcistransferase activity / plastid membrane organization / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / prenyltransferase activity / chloroplast stroma / response to cold / chloroplast / magnesium ion binding
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
DIPHOSPHATE / DIMETHYLALLYL S-THIOLODIPHOSPHATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Dimethylallylcistransferase CPT1, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsImaizumi, R. / Matsuura, H. / Yanai, T. / Takeshita, K. / Misawa, S. / Yamaguchi, H. / Sakai, N. / Miyagi-Inoue, Y. / Suenaga-Hiromori, M. / Kataoka, K. ...Imaizumi, R. / Matsuura, H. / Yanai, T. / Takeshita, K. / Misawa, S. / Yamaguchi, H. / Sakai, N. / Miyagi-Inoue, Y. / Suenaga-Hiromori, M. / Kataoka, K. / Nakayama, T. / Yamamoto, M. / Takahashi, S. / Yamashita, S.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H05470 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
Japan Society for the Promotion of Science (JSPS)22K19143 Japan
Japan Society for the Promotion of Science (JSPS)22KJ1466 Japan
Japan Society for the Promotion of Science (JSPS)20H02909 Japan
Japan Society for the Promotion of Science (JSPS)21H02115 Japan
CitationJournal: Chembiochem / Year: 2024
Title: Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Authors: Imaizumi, R. / Matsuura, H. / Yanai, T. / Takeshita, K. / Misawa, S. / Yamaguchi, H. / Sakai, N. / Miyagi-Inoue, Y. / Suenaga-Hiromori, M. / Waki, T. / Kataoka, K. / Nakayama, T. / Yamamoto, ...Authors: Imaizumi, R. / Matsuura, H. / Yanai, T. / Takeshita, K. / Misawa, S. / Yamaguchi, H. / Sakai, N. / Miyagi-Inoue, Y. / Suenaga-Hiromori, M. / Waki, T. / Kataoka, K. / Nakayama, T. / Yamamoto, M. / Takahashi, S. / Yamashita, S.
History
DepositionNov 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neryl diphosphate synthase 1
B: Neryl diphosphate synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,67310
Polymers69,6002
Non-polymers1,0738
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-52 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.310, 49.230, 121.390
Angle α, β, γ (deg.)90.000, 91.067, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neryl diphosphate synthase 1 / Dimethylallylcistransferase CPT1 / chloroplastic / Cis-prenyltransferase 1 / SlCPT1


Mass: 34799.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: CPT1, NDPS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1K5M2, dimethylallylcistransferase

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Non-polymers , 7 types, 107 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: DL-malic acid, PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 44740 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.994 / Net I/σ(I): 9.7
Reflection shellResolution: 1.92→2.04 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 7185 / CC1/2: 0.771 / Rrim(I) all: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
PHENIX1.20.1-4487refinement
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VPC

7vpc


Resolution: 1.92→49.146 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2566 2237 5 %
Rwork0.219 42503 -
all0.221 --
obs-44740 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.366 Å2
Baniso -1Baniso -2Baniso -3
1--2.084 Å20 Å20.056 Å2
2--5.321 Å20 Å2
3----3.236 Å2
Refinement stepCycle: LAST / Resolution: 1.92→49.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 59 99 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123912
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163734
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6495265
X-RAY DIFFRACTIONr_angle_other_deg0.7351.5748611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.549521
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34710730
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.85710188
X-RAY DIFFRACTIONr_chiral_restr0.0690.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024438
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02890
X-RAY DIFFRACTIONr_nbd_refined0.220.2744
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.23316
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21862
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.26
X-RAY DIFFRACTIONr_nbd_other0.2670.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0350.21
X-RAY DIFFRACTIONr_mcbond_it2.8464.9321867
X-RAY DIFFRACTIONr_mcbond_other2.8464.9311867
X-RAY DIFFRACTIONr_mcangle_it3.898.8222325
X-RAY DIFFRACTIONr_mcangle_other3.8928.8242326
X-RAY DIFFRACTIONr_scbond_it4.0865.2872045
X-RAY DIFFRACTIONr_scbond_other4.0855.2862046
X-RAY DIFFRACTIONr_scangle_it5.7449.5922940
X-RAY DIFFRACTIONr_scangle_other5.7439.5912941
X-RAY DIFFRACTIONr_lrange_it6.73146.0214226
X-RAY DIFFRACTIONr_lrange_other6.72946.0234218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.92-1.970.5581670.6231750.61633420.6670.6181000.61
1.97-2.0240.451560.47829780.47731340.8240.8031000.478
2.024-2.0820.4031550.35229440.35430990.8490.861000.347
2.082-2.1460.3531520.29128750.29430270.8770.8911000.283
2.146-2.2170.321470.26527930.26829400.9090.9291000.255
2.217-2.2940.3221430.25127200.25528630.9240.9441000.237
2.294-2.3810.2581360.24225790.24327150.950.9541000.225
2.381-2.4780.2771320.24625180.24826500.9420.9561000.233
2.478-2.5870.3151260.23923950.24325210.9370.961000.225
2.587-2.7130.2821210.23722900.23924120.9430.96399.95850.229
2.713-2.860.3241160.23722040.24123200.9310.9621000.23
2.86-3.0320.2451090.23620730.23621820.9580.9641000.234
3.032-3.2410.2731030.23519630.23720660.9560.9661000.24
3.241-3.4990.283960.21618160.21919120.9510.9721000.224
3.499-3.8310.231880.18716870.18917750.9660.981000.201
3.831-4.280.197810.16415220.16516030.9770.9831000.19
4.28-4.9360.165720.14613720.14714440.9830.9871000.183
4.936-6.0310.249600.18811520.19112120.9680.9831000.23
6.031-8.4650.226480.28950.2019440.9730.97999.89410.256
8.465-49.1460.181290.1655520.1665820.9840.98199.82820.254

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