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- PDB-3lx6: Crystal structure of putative dna cytosine methylase from shigell... -

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Basic information

Entry
Database: PDB / ID: 3lx6
TitleCrystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T
ComponentsCytosine-specific methyltransferase
KeywordsTRANSFERASE / structural genomics / dcm / Restriction system / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyDNA Methylase; Chain A, domain 2 - #30 / DNA Methylase; Chain A, domain 2 / Vaccinia Virus protein VP39 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2012Group: Database references / Source and taxonomy
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Cytosine-specific methyltransferase
B: Cytosine-specific methyltransferase


Theoretical massNumber of molelcules
Total (without water)94,2472
Polymers94,2472
Non-polymers00
Water52229
1
A: Cytosine-specific methyltransferase


Theoretical massNumber of molelcules
Total (without water)47,1231
Polymers47,1231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytosine-specific methyltransferase


Theoretical massNumber of molelcules
Total (without water)47,1231
Polymers47,1231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.957, 83.807, 113.236
Angle α, β, γ (deg.)90.000, 118.510, 90.000
Int Tables number5
Space group name H-MC121
Detailsunknown

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Components

#1: Protein Cytosine-specific methyltransferase


Mass: 47123.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Gene: dcm, S2100, SF2005, SF2457T_1495 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E3Y0J2, DNA (cytosine-5-)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 10% PEG 8K, 8% Ethylene Glycol, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 43909 / % possible obs: 96.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.083 / Χ2: 1.366 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.20.39222260.755198.2
2.34-2.383.20.34722060.808198.2
2.38-2.433.20.29721980.791198.3
2.43-2.483.20.28522320.856198.3
2.48-2.533.20.25721920.85198.2
2.53-2.593.20.20922350.936198.1
2.59-2.663.20.18221900.989198.1
2.66-2.733.20.14721901.054197.9
2.73-2.813.20.12922171.218197.6
2.81-2.93.20.11722171.283197.5
2.9-33.20.122301.459197.7
3-3.123.20.08721881.499197.1
3.12-3.263.20.08321981.563197
3.26-3.443.20.07321871.584197
3.44-3.653.20.07921841.773196.5
3.65-3.933.20.08221952.153196.3
3.93-4.333.20.07821771.923195.8
4.33-4.953.20.07421901.971195.3
4.95-6.243.10.06321491.904194.3
6.24-503.10.06221082.037189.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXEmodel building
SHELXDphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→31.26 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.302 / WRfactor Rwork: 0.257 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.763 / SU B: 18.944 / SU ML: 0.211 / SU R Cruickshank DPI: 0.323 / SU Rfree: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2214 5 %RANDOM
Rwork0.243 ---
obs0.245 43908 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.47 Å2 / Biso mean: 32.744 Å2 / Biso min: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.85 Å2
2--0.02 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.29→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 0 29 5835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225949
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9518055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22923.033300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40815969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0511555
X-RAY DIFFRACTIONr_chiral_restr0.10.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214630
X-RAY DIFFRACTIONr_mcbond_it0.7331.53648
X-RAY DIFFRACTIONr_mcangle_it1.35625872
X-RAY DIFFRACTIONr_scbond_it2.0932301
X-RAY DIFFRACTIONr_scangle_it3.3414.52183
LS refinement shellResolution: 2.292→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 151 -
Rwork0.286 2966 -
all-3117 -
obs--93.27 %
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)
11.3715-0.3858-1.11590.73541.07053.4313-0.0210.29390.0084-0.10950.07380.0156-0.1265-0.0417-0.05280.0295-0.05840.07080.24750.0080.09285.673-1.596-24.761
21.95240.2089-0.32512.35212.3063.14360.2048-0.19420.16470.2594-0.3920.25430.041-0.21670.18720.1946-0.15430.12170.5158-0.07930.3414-23.042-23.844-31.197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A78 - 462
2X-RAY DIFFRACTION2B78 - 462

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