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- PDB-8kgb: SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP -

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Basic information

Entry
Database: PDB / ID: 8kgb
TitleSlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP
ComponentsDimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
KeywordsTRANSFERASE / cis-prenyltransferase
Function / homology
Function and homology information


dimethylallylcistransferase / dimethylallylcistransferase activity / plastid membrane organization / polyprenyltransferase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / chloroplast stroma / protein glycosylation / response to cold ...dimethylallylcistransferase / dimethylallylcistransferase activity / plastid membrane organization / polyprenyltransferase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / chloroplast stroma / protein glycosylation / 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
GERANYL S-THIOLODIPHOSPHATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Dimethylallylcistransferase CPT1, chloroplastic / Dehydrodolichyl diphosphate synthase 2
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSuenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Yamaguchi, H. / Yanbe, F. / Waki, T. ...Suenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Yamaguchi, H. / Yanbe, F. / Waki, T. / Tozawa, Y. / Miyagi-Inoue, Y. / Yamamoto, M. / Kataoka, K. / Nakayama, T. / Yamashita, S. / Takahashi, 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: To Be Published
Title: A versatile system for enzymatic synthesis of natural and unnatural polyisoprenoids on rubber particles
Authors: Suenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Mikami, T. / Takahashi, T. / Minakawa, C. / Yamaguchi, H. / Yanbe, F. / Waki, T. / ...Authors: Suenaga-Hiromori, M. / Ishii, T. / Imaizumi, R. / Takeshita, K. / Yanai, T. / Matsuura, H. / Sakai, N. / Mikami, T. / Takahashi, T. / Minakawa, C. / Yamaguchi, H. / Yanbe, F. / Waki, T. / Tozawa, Y. / Miyagi-Inoue, Y. / Fushihara, K. / Yamamoto, M. / Kataoka, K. / Nakayama, T. / Yamashita, S. / Takahashi, S.
History
DepositionAug 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
B: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
C: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
D: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,93316
Polymers121,6154
Non-polymers2,31912
Water3,531196
1
A: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
B: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9258
Polymers60,8072
Non-polymers1,1176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-65 kcal/mol
Surface area20000 Å2
MethodPISA
2
C: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
D: Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0098
Polymers60,8072
Non-polymers1,2016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-61 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.540, 126.710, 72.690
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2 / Cis-prenyltransferase 1 / SlCPT1 / Neryl-diphosphate synthase 1


Mass: 30403.678 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato), (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: CPT1, NDPS1, At5g58770, CPT1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C1K5M2, UniProt: Q56Y11, dimethylallylcistransferase
#2: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, malonate 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: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 275956 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rrim(I) all: 0.109 / Net I/σ(I): 11.17
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.22 / Num. unique obs: 44464 / CC1/2: 0.547 / Rrim(I) all: 1.39 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.19.2refinement
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→47.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.677 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23518 2334 5 %RANDOM
Rwork0.18819 ---
obs0.1905 44269 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å20.54 Å2
2--1.23 Å2-0 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 2.32→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7853 0 131 196 8180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138143
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177681
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.64610967
X-RAY DIFFRACTIONr_angle_other_deg1.4451.57917860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73423.201428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.352151539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7431541
X-RAY DIFFRACTIONr_chiral_restr0.0650.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021652
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2535.3923892
X-RAY DIFFRACTIONr_mcbond_other4.2525.3913891
X-RAY DIFFRACTIONr_mcangle_it6.4348.0614851
X-RAY DIFFRACTIONr_mcangle_other6.4348.0624852
X-RAY DIFFRACTIONr_scbond_it4.9515.914251
X-RAY DIFFRACTIONr_scbond_other4.9515.9114252
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8788.6226117
X-RAY DIFFRACTIONr_long_range_B_refined10.80162.4818930
X-RAY DIFFRACTIONr_long_range_B_other10.80462.4828925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 191 -
Rwork0.319 3273 -
obs--99.83 %

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