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- PDB-3e7p: CRYSTAL STRUCTURE OF of putative methyltransferase from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 3e7p
TitleCRYSTAL STRUCTURE OF of putative methyltransferase from Bacteroides vulgatus ATCC 8482
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / putative methyltransferase / NYSGXRC / HYDROLASE / PSI-2
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / 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
Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Toro, R. / 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 of putative methyltransferase from Bacteroides vulgatus ATCC 8482
Authors: Malashkevich, v.n. / Toro, R. / meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 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 1.3Nov 14, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 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: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)30,7801
Polymers30,7801
Non-polymers00
Water3,477193
1
A: Putative methyltransferase

A: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)61,5602
Polymers61,5602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.702, 103.568, 132.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

21A-463-

HOH

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Components

#1: Protein Putative methyltransferase


Mass: 30779.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_3255 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A6L5C0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 45% PPG P400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 30.1 / Number: 155049 / Rmerge(I) obs: 0.053 / Χ2: 1.63 / D res high: 1.89 Å / D res low: 50 Å / Num. obs: 44798 / % possible obs: 75.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.075098.510.0331.8393.7
3.234.0799.410.0472.4623.7
2.823.2399.910.0621.8343.8
2.572.8299.810.091.4923.8
2.382.5793.810.1151.3163.5
2.242.388110.1371.2833.3
2.132.2464.610.161.1813.2
2.042.1352.110.191.2143
1.962.0438.210.2261.0872.8
1.891.9623.510.2850.9832.4
ReflectionResolution: 1.89→50 Å / Num. obs: 44798 / % possible obs: 75.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.053 / Χ2: 1.627
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.89-1.962.40.28513900.983123.5
1.96-2.042.80.22622811.087138.2
2.04-2.1330.1930871.214152.1
2.13-2.243.20.1638841.181164.6
2.24-2.383.30.13748191.283181
2.38-2.573.50.11555831.316193.8
2.57-2.823.80.0959661.492199.8
2.82-3.233.80.06259571.834199.9
3.23-4.073.70.04759482.462199.4
4.07-503.70.03358831.839198.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU B: 5.767 / SU ML: 0.087 / SU R Cruickshank DPI: 0.154 / SU Rfree: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1197 5.1 %RANDOM
Rwork0.184 ---
obs0.186 23357 100 %-
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: 78.77 Å2 / Biso mean: 39.004 Å2 / Biso min: 26.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 193 2223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222110
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.942862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16424.528106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05715354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.608159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211637
X-RAY DIFFRACTIONr_mcbond_it0.9433.51265
X-RAY DIFFRACTIONr_mcangle_it3.734502039
X-RAY DIFFRACTIONr_scbond_it8.29950845
X-RAY DIFFRACTIONr_scangle_it1.114.5819
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 36 -
Rwork0.262 544 -
all-580 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 34.5945 Å / Origin y: 32.2655 Å / Origin z: 49.9133 Å
111213212223313233
T-0.0445 Å2-0.0095 Å20.007 Å2--0.0402 Å2-0.0018 Å2---0.0273 Å2
L0.7762 °2-0.2207 °2-0.1557 °2-0.3841 °20.2469 °2--1.1451 °2
S0.0686 Å °0.1069 Å °-0.0027 Å °-0.0943 Å °0.0307 Å °-0.0145 Å °-0.0161 Å °0.0535 Å °-0.0992 Å °

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