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- PDB-7cc3: Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei... -

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Basic information

Entry
Database: PDB / ID: 7cc3
TitleVersatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG)
Componentscis-prenyltransferase MM_0014
KeywordsTRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / / Isoprenoid / MM_0014 / archaea / farnesylglycerol
Function / homologyUndecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / 3-Layer(aba) Sandwich / Alpha Beta / DIPHOSPHATE / Chem-FQ0 / Chem-FQF / Chem-FV3 / PHOSPHATE ION
Function and homology information
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsUnno, H. / Hemmi, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05437 Japan
Japan Society for the Promotion of Science (JSPS)19H04651 Japan
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations.
Authors: Okada, M. / Unno, H. / Emi, K.I. / Matsumoto, M. / Hemmi, H.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: cis-prenyltransferase MM_0014
B: cis-prenyltransferase MM_0014
C: cis-prenyltransferase MM_0014
D: cis-prenyltransferase MM_0014
E: cis-prenyltransferase MM_0014
F: cis-prenyltransferase MM_0014
G: cis-prenyltransferase MM_0014
H: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,61940
Polymers205,5088
Non-polymers8,11132
Water14,070781
1
A: cis-prenyltransferase MM_0014
B: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42510
Polymers51,3772
Non-polymers2,0488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-20 kcal/mol
Surface area18780 Å2
MethodPISA
2
C: cis-prenyltransferase MM_0014
D: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,34610
Polymers51,3772
Non-polymers1,9698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-31 kcal/mol
Surface area17990 Å2
MethodPISA
3
E: cis-prenyltransferase MM_0014
F: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42510
Polymers51,3772
Non-polymers2,0488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-22 kcal/mol
Surface area18100 Å2
MethodPISA
4
G: cis-prenyltransferase MM_0014
H: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42510
Polymers51,3772
Non-polymers2,0488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-18 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.048, 99.221, 193.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
cis-prenyltransferase MM_0014


Mass: 25688.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 813 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FQ0 / 2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,3-diol


Mass: 296.445 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H32O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FQF / (2R)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol


Mass: 296.445 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H32O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FV3 / (2S)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol


Mass: 296.445 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H32O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→48.5 Å / Num. obs: 202517 / % possible obs: 100 % / Redundancy: 22.3 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Net I/σ(I): 42.6
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 1.84 / Num. unique obs: 9927 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CAQ

7caq


Resolution: 1.72→48.062 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.98 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2129 9998 4.934 %
Rwork0.1963 192628 -
all0.197 --
obs-202517 99.64 %
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: 32.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.024 Å20 Å2
3---0.013 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13859 0 556 781 15196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314723
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714202
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.68519808
X-RAY DIFFRACTIONr_angle_other_deg1.2971.65732830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18451686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75821.788783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63152531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.88415104
X-RAY DIFFRACTIONr_chiral_restr0.0580.21847
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023217
X-RAY DIFFRACTIONr_nbd_refined0.1920.22783
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.213212
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26813
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.26202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2651
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.223
X-RAY DIFFRACTIONr_nbd_other0.1370.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.236
X-RAY DIFFRACTIONr_mcbond_it1.7123.2736786
X-RAY DIFFRACTIONr_mcbond_other1.7123.2736784
X-RAY DIFFRACTIONr_mcangle_it2.5694.98455
X-RAY DIFFRACTIONr_mcangle_other2.5694.98455
X-RAY DIFFRACTIONr_scbond_it1.9763.5267937
X-RAY DIFFRACTIONr_scbond_other1.9763.5267938
X-RAY DIFFRACTIONr_scangle_it3.0955.18911352
X-RAY DIFFRACTIONr_scangle_other3.0955.18811353
X-RAY DIFFRACTIONr_lrange_it5.01737.85616319
X-RAY DIFFRACTIONr_lrange_other4.98837.70416201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7620.1036810.08613502X-RAY DIFFRACTION95.1943
1.762-1.810.1097480.08313783X-RAY DIFFRACTION100
1.81-1.8630.127460.09913418X-RAY DIFFRACTION100
1.863-1.920.1396580.12313023X-RAY DIFFRACTION100
1.92-1.9830.1696370.15212738X-RAY DIFFRACTION100
1.983-2.0520.1986410.17612223X-RAY DIFFRACTION100
2.052-2.130.2196520.19411804X-RAY DIFFRACTION100
2.13-2.2170.2345970.20811406X-RAY DIFFRACTION100
2.217-2.3150.2525320.21310992X-RAY DIFFRACTION100
2.315-2.4280.2345800.21910431X-RAY DIFFRACTION100
2.428-2.560.2255100.2149992X-RAY DIFFRACTION100
2.56-2.7150.2364570.2189464X-RAY DIFFRACTION100
2.715-2.9020.2354750.2238916X-RAY DIFFRACTION100
2.902-3.1340.2534280.238292X-RAY DIFFRACTION100
3.134-3.4330.2324010.2217676X-RAY DIFFRACTION100
3.433-3.8380.2383180.2067015X-RAY DIFFRACTION100
3.838-4.430.1883090.186181X-RAY DIFFRACTION100
4.43-5.4230.1712790.1765260X-RAY DIFFRACTION100
5.423-7.6570.2472170.2174129X-RAY DIFFRACTION100
7.657-48.0620.1971320.192383X-RAY DIFFRACTION99.3678

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