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- PDB-3vc1: Crystal structure of geranyl diphosphate C-methyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 3vc1
TitleCrystal structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor A3(2) in complex with Mg2+, geranyl-S-thiolodiphosphate, and S-adenosyl-L-homocysteine
ComponentsGeranyl diphosphate 2-C-methyltransferase
KeywordsTRANSFERASE / Rossmann fold / methyltransferase fold / SAM-dependent methyltransferase / C-methyltransferase / terpenoid biosynthesis / 2-methylisoborneol biosynthesis
Function / homology
Function and homology information


geranyl diphosphate 2-C-methyltransferase / C-methyltransferase activity / terpene metabolic process / S-adenosyl-L-methionine binding / S-adenosylmethionine-dependent methyltransferase activity / methylation / magnesium ion binding
Similarity search - Function
: / : / Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GERANYL S-THIOLODIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / Geranyl diphosphate 2-C-methyltransferase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.82 Å
AuthorsKoksal, M. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of Geranyl Diphosphate C-Methyltransferase from Streptomyces coelicolor and Implications for the Mechanism of Isoprenoid Modification.
Authors: Koksal, M. / Chou, W.K. / Cane, D.E. / Christianson, D.W.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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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)430,82664
Polymers420,48112
Non-polymers10,34552
Water34,3011904
1
A: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0557
Polymers35,0401
Non-polymers1,0156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9636
Polymers35,0401
Non-polymers9235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0597
Polymers35,0401
Non-polymers1,0196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7794
Polymers35,0401
Non-polymers7393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8715
Polymers35,0401
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.029, 102.903, 203.582
Angle α, β, γ (deg.)90.00, 99.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 35040.090 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: orf4, SCBAC12C8.02, SCO7701 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9F1Y5, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 6 types, 1956 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H20O6P2S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1904 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES (pH 7.5), 25% polyethylene glycol 3350, 200 mM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011
Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 372879 / Num. obs: 348804 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 10.2
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.1 / Num. unique all: 34608 / Rsym value: 0.536 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.82→46.28 Å / SU ML: 0.18 / σ(F): 0.07 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 1859 57 %RANDOM
Rwork0.1667 ---
all0.1669 348804 --
obs0.1669 324579 92.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.024 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8366 Å2-0 Å22.7913 Å2
2---2.2001 Å20 Å2
3----3.6365 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.82→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26616 0 647 1904 29167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01627965
X-RAY DIFFRACTIONf_angle_d1.61137961
X-RAY DIFFRACTIONf_dihedral_angle_d17.92610125
X-RAY DIFFRACTIONf_chiral_restr0.113960
X-RAY DIFFRACTIONf_plane_restr0.0084979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8203-1.86950.26211220.234721095X-RAY DIFFRACTION78
1.8695-1.92450.23691320.217322890X-RAY DIFFRACTION85
1.9245-1.98660.27391360.202723681X-RAY DIFFRACTION88
1.9866-2.05760.22791380.183124225X-RAY DIFFRACTION90
2.0576-2.140.22281510.172824606X-RAY DIFFRACTION92
2.14-2.23740.21341390.170924942X-RAY DIFFRACTION93
2.2374-2.35540.19811440.166525176X-RAY DIFFRACTION94
2.3554-2.50290.20791490.171525432X-RAY DIFFRACTION95
2.5029-2.69620.19961470.165525841X-RAY DIFFRACTION96
2.6962-2.96740.20111470.171525998X-RAY DIFFRACTION96
2.9674-3.39670.17761530.168126019X-RAY DIFFRACTION96
3.3967-4.2790.15911500.141525675X-RAY DIFFRACTION95
4.279-46.29520.16611510.149627140X-RAY DIFFRACTION99

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