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

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Basic information

Entry
Database: PDB / ID: 7caq
TitleVersatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: substrate-free)
Componentscis-prenyltransferase MM_0014
KeywordsTRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / archaea. isoprenoid
Function / homologyUndecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / 3-Layer(aba) Sandwich / Alpha Beta / PALMITIC ACID / PHOSPHATE ION
Function and homology information
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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

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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)51,8235
Polymers51,3772
Non-polymers4463
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-22 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.019, 100.439, 130.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-527-

HOH

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Components

#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) / Gene: MM_0014 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.81 %
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: 1.69→65.3 Å / Num. obs: 59466 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.1
Reflection shellResolution: 1.69→1.78 Å / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 3 / Num. unique obs: 8623 / CC1/2: 0.846

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X07

1x07


Resolution: 1.69→40.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.794 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24766 2945 5 %RANDOM
Rwork0.20883 ---
obs0.21079 56446 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.915 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.69→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 28 298 3710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173302
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6464716
X-RAY DIFFRACTIONr_angle_other_deg1.3451.5797647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95721.667192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88515612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.151526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
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_it3.0383.1871656
X-RAY DIFFRACTIONr_mcbond_other3.0363.1861655
X-RAY DIFFRACTIONr_mcangle_it4.1794.7712063
X-RAY DIFFRACTIONr_mcangle_other4.184.7722064
X-RAY DIFFRACTIONr_scbond_it3.833.6321835
X-RAY DIFFRACTIONr_scbond_other3.8353.6361828
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8015.262642
X-RAY DIFFRACTIONr_long_range_B_refined7.53237.7364036
X-RAY DIFFRACTIONr_long_range_B_other7.50437.3983978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.729 Å
RfactorNum. reflection% reflection
Rfree0.39 197 -
Rwork0.319 4159 -
obs--99.59 %

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