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- PDB-3cbg: Functional and Structural Characterization of a Cationdependent O... -

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Basic information

Entry
Database: PDB / ID: 3cbg
TitleFunctional and Structural Characterization of a Cationdependent O-Methyltransferase from the Cyanobacterium Synechocystis Sp. Strain PCC 6803
ComponentsO-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase / Cyanobacterium
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4FE / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKopycki, J.G. / Neumann, P. / Stubbs, M.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Functional and Structural Characterization of a Cation-dependent O-Methyltransferase from the Cyanobacterium Synechocystis sp. Strain PCC 6803
Authors: Kopycki, J.G. / Stubbs, M.T. / Brandt, W. / Hagemann, M. / Porzel, A. / Schmidt, J. / Schliemann, W. / Zenk, M.H. / Vogt, T.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5405
Polymers25,7431
Non-polymers7974
Water2,234124
1
A: O-methyltransferase
hetero molecules

A: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,07910
Polymers51,4852
Non-polymers1,5948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area4260 Å2
ΔGint-21 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.622, 57.622, 119.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1251-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein O-methyltransferase


Mass: 25742.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 pREP4
References: UniProt: Q55813, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#5: Chemical ChemComp-4FE / (2E)-3-(3-hydroxy-4-methoxyphenyl)prop-2-enoic acid / 3-(3-HYDROXY-4-METHOXYPHENYL)-2-PROPENOIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000 (w/v), 0.2M MgCl2 in 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -h,-k,l / Fraction: 0.284
ReflectionResolution: 2→30 Å / Num. obs: 16207 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.124 / Χ2: 1.063 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.076.90.70315701.13199.9
2.07-2.158.60.55115821.113100
2.15-2.258.90.42915821.165100
2.25-2.378.90.33716071.174100
2.37-2.5290.2616121.049100
2.52-2.7190.19715901.166100
2.71-2.9990.14716271.118100
2.99-3.4290.10716280.9100
3.42-4.3190.08116450.934100
4.31-308.50.07117640.919100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.96 Å
Translation2.5 Å29.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3c3y

3c3y


Resolution: 2→28.81 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: hemihedrally twinned; THIS IS A TWINNED DATA. THE TWINNING OPERATOR IS (H,K,L) -> (-h, -k, l) AND THE TWINNING FRACTION IS 0.284.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1485 9.2 %RANDOM
Rwork0.152 ---
obs0.156 16164 99.9 %-
all-16207 --
Solvent computationBsol: 46.447 Å2
Displacement parametersBiso mean: 28.886 Å2
Baniso -1Baniso -2Baniso -3
1--2.187 Å2-2.302 Å20 Å2
2---2.187 Å20 Å2
3---4.373 Å2
Refinement stepCycle: LAST / Resolution: 2→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 55 124 1882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.235
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2Syn_lig.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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