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- PDB-8x37: Neryl diphosphate synthase from Solanum lycopersicum complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8x37
TitleNeryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP
ComponentsNeryl-diphosphate synthase 1
KeywordsTRANSFERASE / cis-prenyltransferase
Function / homology
Function and homology information


dimethylallylcistransferase / dimethylallylcistransferase activity / plastid membrane organization / polyprenol biosynthetic process / 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
DIMETHYLALLYL S-THIOLODIPHOSPHATE / Dimethylallylcistransferase CPT1, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)61,4169
Polymers60,2952
Non-polymers1,1227
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-72 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.260, 50.270, 120.250
Angle α, β, γ (deg.)90.000, 91.327, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 53 - 299 / Label seq-ID: 12 - 258

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 30147.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GTMSARGLNKISCSL NLQTEKLCYEDNDNDLDEELMPKHIALIMDGNRRWAKDKGLEVYEGHKHIIPKLKEICDISSKLGIQIITAFAFSTENWKRSKEEVDFLL ...Details: GTMSARGLNKISCSL NLQTEKLCYEDNDNDLDEELMPKHIALIMDGNRRWAKDKGLEVYEGHKHIIPKLKEICDISSKLGIQIITAFAFSTENWKRSKEEVDFLL QMFEEIYDEFSRSGVRVSIIGCKSDLPMTLQKCIALTEETTKGNKGLHLVIALNYGGYYDILQATKSIVNKAMNGLLDVEDINKNLFDQE LESKCPNPDLLIRTGGEQRVSNFLLWQLAYTEFYFTNTLFPDFGEEDLKEAIMNFQQRHRRFGGHTY
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: CPT1, NDPS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1K5M2, dimethylallylcistransferase
#2: Chemical
ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, DL-Malic acid

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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: 1.98→50 Å / Num. obs: 41220 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.993 / Rrim(I) all: 0.124 / Net I/σ(I): 8.52
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 6606 / CC1/2: 0.75 / Rrim(I) all: 2.65 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHENIX1.20.1-4487refinement
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VPC

7vpc


Resolution: 1.98→49.165 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: FREE R-VALUE / ESU R: 0.183 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2744 2061 5 %
Rwork0.2213 39159 -
all0.224 --
obs-41220 99.944 %
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: 64.711 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å2-0 Å20.624 Å2
2--7.077 Å2-0 Å2
3----4.681 Å2
Refinement stepCycle: LAST / Resolution: 1.98→49.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 59 45 3922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123956
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163797
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.8465326
X-RAY DIFFRACTIONr_angle_other_deg0.7451.7798752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.061525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41310743
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2910189
X-RAY DIFFRACTIONr_chiral_restr0.0680.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024535
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02901
X-RAY DIFFRACTIONr_nbd_refined0.2280.2774
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.23314
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21863
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.430.24
X-RAY DIFFRACTIONr_nbd_other0.2710.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.23
X-RAY DIFFRACTIONr_mcbond_it4.9486.1711887
X-RAY DIFFRACTIONr_mcbond_other4.9476.171887
X-RAY DIFFRACTIONr_mcangle_it6.96911.0662350
X-RAY DIFFRACTIONr_mcangle_other6.96911.0672351
X-RAY DIFFRACTIONr_scbond_it5.9536.7932069
X-RAY DIFFRACTIONr_scbond_other5.9526.7942070
X-RAY DIFFRACTIONr_scangle_it9.08312.272976
X-RAY DIFFRACTIONr_scangle_other9.08212.272977
X-RAY DIFFRACTIONr_lrange_it11.08456.6244244
X-RAY DIFFRACTIONr_lrange_other11.08656.6374242
X-RAY DIFFRACTIONr_ncsr_local_group_10.1370.056911
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.137150.05007
12AX-RAY DIFFRACTIONLocal ncs0.137150.05007
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
1.98-2.0310.5651490.61128440.60929970.6380.63499.86650.604
2.031-2.0870.5161480.51528070.51529550.6980.6741000.515
2.087-2.1470.4311440.43827350.43828800.7160.68699.96530.436
2.147-2.2130.3561390.37926500.37727890.8110.8041000.37
2.213-2.2860.381350.34925620.35126980.8290.84199.96290.339
2.286-2.3660.3111310.33124730.3326040.9230.8911000.317
2.366-2.4550.3751250.30623930.30925180.8640.9181000.288
2.455-2.5550.2671220.25323050.25424270.9440.9491000.239
2.555-2.6680.2891170.24822230.2523410.9380.95599.95730.239
2.668-2.7980.3641130.24921440.25522580.9110.95499.95570.237
2.798-2.9490.3371050.2720030.27421090.9260.95199.95260.262
2.949-3.1270.3311000.24919070.25320070.9280.9591000.242
3.127-3.3420.295960.22818150.23219140.9440.96799.84330.232
3.342-3.6080.228880.21116760.21117640.9640.9761000.221
3.608-3.950.276830.19615650.216480.9610.9791000.213
3.95-4.4130.25730.15813890.16214630.9630.98499.93160.186
4.413-5.0890.188660.13912600.14213260.9790.9891000.177
5.089-6.2160.259570.16310770.16811340.9670.9861000.201
6.216-8.7210.184440.1648340.1658780.980.9861000.216
8.721-49.1650.184260.164950.1615260.980.98499.04940.249

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