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

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Basic information

Entry
Database: PDB / ID: 7cav
TitleVersatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG+DMAPP)
Componentscis-prenyltransferase MM_0014
KeywordsTRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / Isoprenoid / MM_0014 / archaea / farnesylglycerol
Function / homologyDIMETHYLALLYL DIPHOSPHATE / DIPHOSPHATE / Chem-FQ0 / PHOSPHATE ION
Function and homology information
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 10, 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)210,16936
Polymers205,5088
Non-polymers4,66228
Water8,737485
1
A: cis-prenyltransferase MM_0014
B: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5629
Polymers51,3772
Non-polymers1,1857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-32 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)52,4108
Polymers51,3772
Non-polymers1,0336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-37 kcal/mol
Surface area18120 Å2
MethodPISA
3
E: cis-prenyltransferase MM_0014
F: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5629
Polymers51,3772
Non-polymers1,1857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-34 kcal/mol
Surface area17720 Å2
MethodPISA
4
G: cis-prenyltransferase MM_0014
H: cis-prenyltransferase MM_0014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63510
Polymers51,3772
Non-polymers1,2588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-32 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.853, 98.910, 193.853
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, 513 molecules

#2: Chemical
ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 4 / Source method: obtained synthetically / Formula: C18H32O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsThe Genebank accession number is 24771896 for the protein.

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol, 3 mM farnesyl pyrophosphate (FPP), 0.3 mM MgCl2

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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: 1.91→48.46 Å / Num. obs: 147512 / % possible obs: 100 % / Redundancy: 22.3 % / CC1/2: 0.688 / Net I/σ(I): 33.6
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 2.05 / Num. unique obs: 7217 / CC1/2: 0.688

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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: 1.91→47.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2195 7541 5.114 %
Rwork0.1963 139929 -
all0.197 --
obs-147470 99.814 %
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: 42.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å20 Å20 Å2
2--0.007 Å20 Å2
3----0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.91→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13896 0 272 485 14653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01314473
X-RAY DIFFRACTIONr_bond_other_d0.0340.01713649
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.65819570
X-RAY DIFFRACTIONr_angle_other_deg2.2631.59531587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38851691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60921.669791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.048152535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.89815104
X-RAY DIFFRACTIONr_chiral_restr0.0630.21839
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215858
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023170
X-RAY DIFFRACTIONr_nbd_refined0.1970.22809
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.212566
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26853
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0620.26111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2553
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.219
X-RAY DIFFRACTIONr_nbd_other0.2010.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.227
X-RAY DIFFRACTIONr_mcbond_it2.5814.316809
X-RAY DIFFRACTIONr_mcbond_other2.5814.3096808
X-RAY DIFFRACTIONr_mcangle_it3.5596.4488485
X-RAY DIFFRACTIONr_mcangle_other3.5596.4498486
X-RAY DIFFRACTIONr_scbond_it2.8774.6887664
X-RAY DIFFRACTIONr_scbond_other2.8444.687605
X-RAY DIFFRACTIONr_scangle_it4.3176.88111085
X-RAY DIFFRACTIONr_scangle_other4.36.86810989
X-RAY DIFFRACTIONr_lrange_it6.19749.77816150
X-RAY DIFFRACTIONr_lrange_other6.18549.67916077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.9590.0925100.06510044X-RAY DIFFRACTION98.0946
1.959-2.0120.14790.07610058X-RAY DIFFRACTION99.8578
2.012-2.070.1395220.1159728X-RAY DIFFRACTION99.8344
2.07-2.1340.1545770.1359370X-RAY DIFFRACTION99.9096
2.134-2.2040.2034620.1659218X-RAY DIFFRACTION99.9174
2.204-2.2810.2314510.1878889X-RAY DIFFRACTION99.9893
2.281-2.3670.2184420.1898639X-RAY DIFFRACTION99.978
2.367-2.4640.2224600.1988225X-RAY DIFFRACTION100
2.464-2.5740.2574370.2167907X-RAY DIFFRACTION100
2.574-2.6990.2354260.2177621X-RAY DIFFRACTION100
2.699-2.8450.2764370.2327193X-RAY DIFFRACTION100
2.845-3.0170.2683530.2296883X-RAY DIFFRACTION100
3.017-3.2260.233580.2296431X-RAY DIFFRACTION100
3.226-3.4840.243260.2256005X-RAY DIFFRACTION100
3.484-3.8160.2433030.2155609X-RAY DIFFRACTION100
3.816-4.2650.2082350.195094X-RAY DIFFRACTION100
4.265-4.9230.1942410.1754488X-RAY DIFFRACTION100
4.923-6.0260.2542350.2043790X-RAY DIFFRACTION100
6.026-8.5060.1911840.2062988X-RAY DIFFRACTION100
8.506-47.920.1761030.1781749X-RAY DIFFRACTION99.0374

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