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- PDB-4f84: Structure analysis of Geranyl diphosphate methyltransferase in co... -

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Basic information

Entry
Database: PDB / ID: 4f84
TitleStructure analysis of Geranyl diphosphate methyltransferase in complex with SAM
ComponentsGeranyl diphosphate 2-C-methyltransferase
KeywordsTRANSFERASE / alpha/beta / Rossmann Fold / methyltransferase
Function / homology
Function and homology information


geranyl diphosphate 2-C-methyltransferase / C-methyltransferase activity / terpene metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / methylation / magnesium ion binding
Similarity search - Function
: / : / Mycolic acid cyclopropane synthetase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Geranyl diphosphate 2-C-methyltransferase
Similarity search - Component
Biological speciesStreptomyces lasaliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAriyawutthiphan, O. / Ose, T. / Minami, A. / Gao, Y.G. / Yao, M. / Oikawa, H. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation
Authors: Ariyawutthiphan, O. / Ose, T. / Minami, A. / Sinde, S. / Tsuda, M. / Gao, Y.-G. / Yao, M. / Oikawa, H. / Tanaka, I.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4912
Polymers35,0921
Non-polymers3981
Water1086
1
A: Geranyl diphosphate 2-C-methyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)212,94312
Polymers210,5526
Non-polymers2,3916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)147.942, 147.942, 66.467
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Geranyl diphosphate 2-C-methyltransferase / SAM dependent methyltransferase / GPP methyltransferase


Mass: 35092.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasaliensis (bacteria) / Gene: gdpmt / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D3KYU3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 1M ammonium suflate, 8% glycerol, 0.1M Tris-HCl, 10mM SAM, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2008 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22017 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2174 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bus

3bus


Resolution: 2.2→33.23 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2284485 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1146 5.2 %RANDOM
Rwork0.261 ---
obs0.261 21970 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9767 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 112.22 Å2 / Biso mean: 64.8819 Å2 / Biso min: 45.01 Å2
Baniso -1Baniso -2Baniso -3
1-15.41 Å2-0 Å20 Å2
2--15.41 Å20 Å2
3----30.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 20 6 1963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.508 104 4.8 %
Rwork0.502 2068 -
all-2172 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6SAM.paramSAM.top

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