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

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Basic information

Entry
Database: PDB / ID: 7car
TitleVersatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: free+IPP)
Componentscis-prenyltransferase, MM_0014
KeywordsTRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / IPP / Isoprenoid / MM_0014 / archaea
Function / homology3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / PALMITIC ACID / PHOSPHATE ION
Function and homology information
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)52,0696
Polymers51,3772
Non-polymers6924
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.940, 100.420, 129.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A16 - 65
2111B16 - 65
1211A80 - 125
2211B80 - 125
1311A160 - 220
2311B160 - 220
1411A67 - 78
2411B67 - 78

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.397643, 0.830639, 0.389769), (0.837546, 0.155122, 0.523883), (0.374696, 0.534768, -0.757381)-3.20734, -1.02901, 7.08155

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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) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.53 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: 1.98→64.8 Å / Num. obs: 36516 / % possible obs: 99.8 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.1
Reflection shellResolution: 1.98→2.09 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 5267 / CC1/2: 0.856

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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: 1.98→39.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25878 1847 5.1 %RANDOM
Rwork0.21953 ---
obs0.22145 34644 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.366 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.98→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 42 147 3545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133475
X-RAY DIFFRACTIONr_bond_other_d0.0340.0173286
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6484695
X-RAY DIFFRACTIONr_angle_other_deg2.2391.587610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5485407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00621.675191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55715610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4751526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023807
X-RAY DIFFRACTIONr_gen_planes_other0.010.02767
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_it3.6714.3731640
X-RAY DIFFRACTIONr_mcbond_other3.6684.3711639
X-RAY DIFFRACTIONr_mcangle_it5.1756.5462043
X-RAY DIFFRACTIONr_mcangle_other5.1756.5482044
X-RAY DIFFRACTIONr_scbond_it4.3124.9341835
X-RAY DIFFRACTIONr_scbond_other4.3124.9391828
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6527.1922641
X-RAY DIFFRACTIONr_long_range_B_refined9.30351.1563954
X-RAY DIFFRACTIONr_long_range_B_other9.30851.1183937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2693 / Type: tight thermal / Rms dev position: 7.05 Å / Weight position: 0.5
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 122 -
Rwork0.309 2543 -
obs--99.48 %

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