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- PDB-4f86: Structure analysis of Geranyl diphosphate methyltransferase in co... -

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Basic information

Entry
Database: PDB / ID: 4f86
TitleStructure analysis of Geranyl diphosphate methyltransferase in complex with GPP and sinefungin
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
GERANYL DIPHOSPHATE / SINEFUNGIN / Geranyl diphosphate 2-C-methyltransferase
Similarity search - Component
Biological speciesStreptomyces lasaliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: Geranyl diphosphate 2-C-methyltransferase
B: Geranyl diphosphate 2-C-methyltransferase
C: Geranyl diphosphate 2-C-methyltransferase
D: Geranyl diphosphate 2-C-methyltransferase
E: Geranyl diphosphate 2-C-methyltransferase
F: Geranyl diphosphate 2-C-methyltransferase
G: Geranyl diphosphate 2-C-methyltransferase
H: Geranyl diphosphate 2-C-methyltransferase
I: Geranyl diphosphate 2-C-methyltransferase
J: Geranyl diphosphate 2-C-methyltransferase
K: Geranyl diphosphate 2-C-methyltransferase
L: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,74448
Polymers421,10512
Non-polymers8,63936
Water0
1
A: Geranyl diphosphate 2-C-methyltransferase
B: Geranyl diphosphate 2-C-methyltransferase
C: Geranyl diphosphate 2-C-methyltransferase
D: Geranyl diphosphate 2-C-methyltransferase
E: Geranyl diphosphate 2-C-methyltransferase
F: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,87224
Polymers210,5526
Non-polymers4,31918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Geranyl diphosphate 2-C-methyltransferase
H: Geranyl diphosphate 2-C-methyltransferase
I: Geranyl diphosphate 2-C-methyltransferase
J: Geranyl diphosphate 2-C-methyltransferase
K: Geranyl diphosphate 2-C-methyltransferase
L: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,87224
Polymers210,5526
Non-polymers4,31918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.937, 87.731, 160.222
Angle α, β, γ (deg.)100.01, 96.65, 90.89
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35092.070 Da / Num. of mol.: 12
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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical
ChemComp-GPP / GERANYL DIPHOSPHATE / Geranyl pyrophosphate


Mass: 314.209 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H20O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.3M lithium sulfate, 1mM sperminero, 30mM magnesium chloride, 50mM sodium cacodylate, pH 6.7, 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: Nov 21, 2009 / Details: mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 82669 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.118
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4153 / % possible all: 95.8

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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: 3→46.51 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2735189 / 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
Rfree0.298 4058 5 %RANDOM
Rwork0.279 ---
obs-80529 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: -6.8095 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 98.47 Å2 / Biso mean: 50.5488 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1--16.41 Å2-6.32 Å23.42 Å2
2--39.12 Å2-10.51 Å2
3----22.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.89 Å
Refinement stepCycle: LAST / Resolution: 3→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25514 0 564 0 26078
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.436 402 5 %
Rwork0.435 7599 -
all-8001 -
obs--95.5 %
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 DIFFRACTION6sin_drg.paramsin_drg.top
X-RAY DIFFRACTION7GPP.paramGPP.top

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