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

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Basic information

Entry
Database: PDB / ID: 7cpm
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: 2.6 Å
AuthorsKurokawa, H. / Ambo, T. / Takahashi, 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)


Theoretical massNumber of molelcules
Total (without water)195,8756
Polymers195,8756
Non-polymers00
Water3,441191
1
A: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)
B: Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)


Theoretical massNumber of molelcules
Total (without water)65,2922
Polymers65,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-13 kcal/mol
Surface area20840 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)


Theoretical massNumber of molelcules
Total (without water)65,2922
Polymers65,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-14 kcal/mol
Surface area20100 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)


Theoretical massNumber of molelcules
Total (without water)65,2922
Polymers65,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-13 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.862, 137.590, 168.854
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: 32645.795 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M citric acid sodium citrate, 5% PEG6000

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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: Nov 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.409 Å / Num. obs: 52305 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 46.201
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 5.124 / Num. unique obs: 5149 / % possible all: 100

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Processing

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

1f75


Resolution: 2.6→49.409 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.19 / Average fsc free: 0.9125 / Average fsc work: 0.9294 / Cross valid method: FREE R-VALUE / ESU R: 1.173 / ESU R Free: 0.302
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2336 2479 4.809 %
Rwork0.189 49069 -
all0.191 --
obs-51548 99.833 %
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: 63.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.996 Å20 Å2-0 Å2
2---2.748 Å20 Å2
3---0.752 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11544 0 0 191 11735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311871
X-RAY DIFFRACTIONr_bond_other_d0.0350.01710786
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.64916163
X-RAY DIFFRACTIONr_angle_other_deg2.3151.57424743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90251456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60619.317732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.467151780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77415148
X-RAY DIFFRACTIONr_chiral_restr0.060.21476
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213617
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022923
X-RAY DIFFRACTIONr_nbd_refined0.20.22257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.29388
X-RAY DIFFRACTIONr_nbtor_refined0.1620.25638
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2256
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.213
X-RAY DIFFRACTIONr_nbd_other0.2220.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.23
X-RAY DIFFRACTIONr_mcbond_it5.4716.6015842
X-RAY DIFFRACTIONr_mcbond_other5.4686.6015841
X-RAY DIFFRACTIONr_mcangle_it7.8799.8997292
X-RAY DIFFRACTIONr_mcangle_other7.889.8997293
X-RAY DIFFRACTIONr_scbond_it5.6027.0886029
X-RAY DIFFRACTIONr_scbond_other5.6027.0886030
X-RAY DIFFRACTIONr_scangle_it8.52710.4298871
X-RAY DIFFRACTIONr_scangle_other8.52510.4298871
X-RAY DIFFRACTIONr_lrange_it11.26775.74112983
X-RAY DIFFRACTIONr_lrange_other11.2775.73212963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.3291750.2623575X-RAY DIFFRACTION100
2.667-2.740.2831710.2463490X-RAY DIFFRACTION100
2.74-2.8190.2931720.223410X-RAY DIFFRACTION100
2.819-2.9060.2871880.213257X-RAY DIFFRACTION100
2.906-3.0010.2691470.2083189X-RAY DIFFRACTION100
3.001-3.1060.2711440.23134X-RAY DIFFRACTION100
3.106-3.2220.271470.2063011X-RAY DIFFRACTION100
3.222-3.3530.2431440.1982875X-RAY DIFFRACTION100
3.353-3.5020.2731560.1952741X-RAY DIFFRACTION100
3.502-3.6720.2791530.2092654X-RAY DIFFRACTION100
3.672-3.8690.2211180.1892533X-RAY DIFFRACTION99.9623
3.869-4.1020.1941190.172403X-RAY DIFFRACTION99.9604
4.102-4.3840.1821080.1652266X-RAY DIFFRACTION99.9579
4.384-4.7320.2211000.1562130X-RAY DIFFRACTION99.9552
4.732-5.1790.1991110.1641945X-RAY DIFFRACTION100
5.179-5.7820.276970.1891789X-RAY DIFFRACTION100
5.782-6.6610.239810.2141579X-RAY DIFFRACTION100
6.661-8.1210.218590.1871385X-RAY DIFFRACTION99.8617
8.121-11.3330.141610.141052X-RAY DIFFRACTION98.0617
11.333-49.4090.242280.244637X-RAY DIFFRACTION93.5302

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