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

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Basic information

Entry
Database: PDB / ID: 7cas
TitleVersatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: free+PPi)
Componentscis-prenyltransferase MM_0014
KeywordsTRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / PPi / Isoprenoid / MM_0014 / archaea
Function / homologyUndecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / 3-Layer(aba) Sandwich / Alpha Beta / DIPHOSPHATE / PALMITIC ACID / PHOSPHATE ION
Function and homology information
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9276
Polymers51,3772
Non-polymers5504
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-25 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.779, 100.219, 130.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cis-prenyltransferase MM_0014


Mass: 25688.492 Da / Num. of mol.: 2
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 , 5 types, 105 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 4 mM cobalt (II) chloride, 4 mM nickel (II) chloride, 4 mM cadmium chloride, 4 mM magnesium chloride, 0.075 M HEPES, pH7.5, 9% PEG 3350, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→65 Å / Num. obs: 24258 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.3
Reflection shellResolution: 2.28→2.4 Å / Rmerge(I) obs: 0.697 / Num. unique obs: 3470 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CAQ

7caq


Resolution: 2.28→65.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.707 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25812 1247 5.1 %RANDOM
Rwork0.22 ---
obs0.22192 22983 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.784 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.28→65.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 33 101 3540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133521
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173329
X-RAY DIFFRACTIONr_angle_refined_deg1.011.6484753
X-RAY DIFFRACTIONr_angle_other_deg0.991.587712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10321.667192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6315620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.531526
X-RAY DIFFRACTIONr_chiral_restr0.0230.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023865
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02777
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_it1.9724.7361669
X-RAY DIFFRACTIONr_mcbond_other1.9664.7341668
X-RAY DIFFRACTIONr_mcangle_it3.4227.0922081
X-RAY DIFFRACTIONr_mcangle_other3.4217.0942082
X-RAY DIFFRACTIONr_scbond_it1.8594.9811852
X-RAY DIFFRACTIONr_scbond_other1.8494.9881841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2537.3412654
X-RAY DIFFRACTIONr_long_range_B_refined6.23153.233947
X-RAY DIFFRACTIONr_long_range_B_other6.21753.1923932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.336 Å
RfactorNum. reflection% reflection
Rfree0.309 88 -
Rwork0.284 1661 -
obs--99.89 %

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