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- PDB-7cpn: CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 7cpn
TitleCRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA
ComponentsTrans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific] / Z-farnesyl diphosphate synthase activity / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / prenyltransferase activity / manganese ion binding / magnesium ion binding / plasma membrane / cytosol
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
Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKurokawa, H. / Ambo, T. / Takahasi, S. / Koyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26450115 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity.
Authors: Kurokawa, H. / Ambo, T. / Takahashi, S. / Koyama, T.
History
DepositionAug 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
B: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
C: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
D: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
E: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
F: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,43220
Polymers192,0916
Non-polymers1,34114
Water7,314406
1
A: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
B: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6038
Polymers64,0302
Non-polymers5726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-90 kcal/mol
Surface area19710 Å2
MethodPISA
2
C: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
D: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4146
Polymers64,0302
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-70 kcal/mol
Surface area19620 Å2
MethodPISA
3
E: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
F: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4146
Polymers64,0302
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-73 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.095, 137.878, 168.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific) / Cis-prenyltransferase / Dodecaprenyl diphosphate synthase


Mass: 32015.104 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_0853 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47RM6, trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific]
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M citric acid sodium citrate pH 5.0, 0.7 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→47.534 Å / Num. obs: 77502 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 63.647
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 8.564 / Num. unique obs: 3826 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F75

1f75


Resolution: 2.28→47.534 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.207 / Average fsc free: 0.9117 / Average fsc work: 0.9275 / Cross valid method: FREE R-VALUE / ESU R: 0.312 / ESU R Free: 0.222
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2394 3830 5.019 %
Rwork0.2028 72481 -
all0.205 --
obs-76311 99.877 %
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: 53.909 Å2
Baniso -1Baniso -2Baniso -3
1-0.595 Å20 Å2-0 Å2
2---0.417 Å20 Å2
3----0.178 Å2
Refinement stepCycle: LAST / Resolution: 2.28→47.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11068 0 71 406 11545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311413
X-RAY DIFFRACTIONr_bond_other_d0.0350.01710414
X-RAY DIFFRACTIONr_angle_refined_deg1.411.64615503
X-RAY DIFFRACTIONr_angle_other_deg2.3091.57623838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78451375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03119.21734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27151769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.23715152
X-RAY DIFFRACTIONr_chiral_restr0.070.21399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213006
X-RAY DIFFRACTIONr_gen_planes_other0.0130.022874
X-RAY DIFFRACTIONr_nbd_refined0.2050.22137
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.29257
X-RAY DIFFRACTIONr_nbtor_refined0.1630.25480
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.25256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2394
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.218
X-RAY DIFFRACTIONr_nbd_other0.2260.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.29
X-RAY DIFFRACTIONr_mcbond_it4.9335.4165524
X-RAY DIFFRACTIONr_mcbond_other4.9285.4155523
X-RAY DIFFRACTIONr_mcangle_it7.0088.1136891
X-RAY DIFFRACTIONr_mcangle_other7.0098.1146892
X-RAY DIFFRACTIONr_scbond_it5.4646.1175889
X-RAY DIFFRACTIONr_scbond_other5.3746.0885838
X-RAY DIFFRACTIONr_scangle_it8.2478.9128612
X-RAY DIFFRACTIONr_scangle_other8.28.878535
X-RAY DIFFRACTIONr_lrange_it10.83662.48712703
X-RAY DIFFRACTIONr_lrange_other10.83662.48712704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3390.3032600.2495265X-RAY DIFFRACTION99.9096
2.339-2.4030.3042590.2365155X-RAY DIFFRACTION99.9077
2.403-2.4720.3032640.2345035X-RAY DIFFRACTION99.8681
2.472-2.5480.2772250.2174924X-RAY DIFFRACTION99.903
2.548-2.6320.292660.224690X-RAY DIFFRACTION99.9194
2.632-2.7240.2782440.2294597X-RAY DIFFRACTION99.9174
2.724-2.8260.2652520.2164410X-RAY DIFFRACTION99.9143
2.826-2.9410.2552240.2114244X-RAY DIFFRACTION99.9106
2.941-3.0710.2542160.2194087X-RAY DIFFRACTION99.9535
3.071-3.2210.252340.2093884X-RAY DIFFRACTION99.9515
3.221-3.3940.2392010.2043762X-RAY DIFFRACTION99.9244
3.394-3.5990.221920.2033531X-RAY DIFFRACTION99.9463
3.599-3.8460.2261720.1943338X-RAY DIFFRACTION100
3.846-4.1520.2291740.1823118X-RAY DIFFRACTION99.8786
4.152-4.5440.1791390.1662885X-RAY DIFFRACTION99.7361
4.544-5.0750.2121500.1722634X-RAY DIFFRACTION99.7849
5.075-5.8490.2421120.2022330X-RAY DIFFRACTION99.8365
5.849-7.1360.271100.2362008X-RAY DIFFRACTION99.8586
7.136-9.9810.208840.1831590X-RAY DIFFRACTION99.8211
9.981-47.5340.224510.23965X-RAY DIFFRACTION99.4129

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