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- PDB-3dp7: CRYSTAL STRUCTURE OF SAM-dependent methyltransferase from Bactero... -

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Basic information

Entry
Database: PDB / ID: 3dp7
TitleCRYSTAL STRUCTURE OF SAM-dependent methyltransferase from Bacteroides vulgatus ATCC 8482
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH / SAM-dependent methyltransferase =CONSORTIUM / NYSGXRC / Methyltransferase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1390 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1390 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SAM-dependent methyltransferase
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsMalashkevich, V.N. / Toro, R. / Ramagopal, U. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF SAM-dependent methyltransferase from Bacteroides vulgatus ATCC 8482
Authors: MALASHKEVICH, V.N. / TORO, R. / Ramagopal, U. / MEYER, A.J. / SAUDER, J.M. / BURLEY, S.K. / ALMO, S.C.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Apr 11, 2012Group: Data collection
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase


Theoretical massNumber of molelcules
Total (without water)82,8722
Polymers82,8722
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-56 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.804, 130.804, 122.747
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 41435.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_1015 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A6KZ44
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M sodium citrate, 0.1 M tris ph 7.0, 0.2 M nacl, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 10.9 / Number: 272651 / Rmerge(I) obs: 0.121 / Χ2: 5.32 / D res high: 2.33 Å / D res low: 50 Å / Num. obs: 65572 / % possible obs: 65.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.025010010.09112.6714.7
3.985.0210010.1219.1284.7
3.483.9810010.1354.3714.8
3.163.4810010.1971.8574.7
2.943.1698.510.3320.9464.3
2.762.9477.910.3980.813.1
2.622.7648.810.4460.7112.1
2.512.6218.610.6260.7831.5
2.412.515.610.7481.2
2.332.411.810.5951.1
ReflectionResolution: 2.33→50 Å / Num. obs: 65572 / % possible obs: 65.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.121 / Χ2: 5.323 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.33-2.411.11810.59511.8
2.41-2.511.25700.74815.6
2.51-2.621.518750.783118.60.626
2.62-2.762.149110.711148.80.446
2.76-2.943.178440.81177.90.398
2.94-3.164.398910.946198.50.332
3.16-3.484.7100791.85711000.197
3.48-3.984.8100944.37111000.135
3.98-5.024.7100519.12811000.121
5.02-504.71007612.67111000.091

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→19.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 18.709 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1671 5.1 %RANDOM
Rwork0.183 ---
obs0.187 32966 64.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 187.8 Å2 / Biso mean: 64.531 Å2 / Biso min: 29.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.33→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 0 90 5694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225721
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9487726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5845699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48824.421285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.307151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5411534
X-RAY DIFFRACTIONr_chiral_restr0.1040.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024348
X-RAY DIFFRACTIONr_mcbond_it0.8453.53463
X-RAY DIFFRACTIONr_mcangle_it4.692505554
X-RAY DIFFRACTIONr_scbond_it11.292502258
X-RAY DIFFRACTIONr_scangle_it0.6944.52172
LS refinement shellResolution: 2.332→2.392 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 3 -
Rwork0.387 56 -
all-59 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.91610.60480.13321.448-0.9122.54120.2628-0.2369-0.00750.3025-0.07630.2313-0.10410.0231-0.1866-0.05750.03170.0242-0.14750.0439-0.048649.121816.345449.7723
20.8568-0.16260.2080.7491-0.89471.80520.05860.1677-0.0614-0.02430.19610.26070.0198-0.1056-0.2547-0.09170.0205-0.0413-0.17350.0651-0.013340.601332.099416.8488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 3555 - 355
2X-RAY DIFFRACTION2BB6 - 3556 - 355

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