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- PDB-3me5: Crystal structure of putative dna cytosine methylase from shigell... -

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Basic information

Entry
Database: PDB / ID: 3me5
TitleCrystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T
ComponentsCytosine-specific methyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / cytosine methylase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


434 Repressor (Amino-terminal Domain) - #140 / DNA Methylase; Chain A, domain 2 - #30 / DNA Methylase; Chain A, domain 2 / 434 Repressor (Amino-terminal Domain) / Vaccinia Virus protein VP39 / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsRamagopal, U.A. / Malashkevich, V.N. / Toro, R. / 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 putative dna cytosine methylase from shigella flexneri 2a str. 2457T
Authors: Ramagopal, U.A. / Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 23, 2012Group: Database references / Source and taxonomy
Revision 1.3Nov 8, 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 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosine-specific methyltransferase


Theoretical massNumber of molelcules
Total (without water)55,2721
Polymers55,2721
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.629, 51.593, 63.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cytosine-specific methyltransferase


Mass: 55272.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Gene: AAP17376.1, dcm, S2100, SF2005, SF2457T_1495 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: E3Y0J2, DNA (cytosine-5-)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 25% PEG 3350, 200mM Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 50037 / % possible obs: 99.9 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.079 / Χ2: 1.442 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.7810.40.93624971.2531100
1.78-1.8111.70.85224371.2921100
1.81-1.8511.90.70124851.2981100
1.85-1.89120.76324471.4761100
1.89-1.9312.10.3924561.6391100
1.93-1.9712.10.46824871.4861100
1.97-2.0212.10.34824671.4351100
2.02-2.0712.10.25124731.4041100
2.07-2.1412.10.20924731.3661100
2.14-2.211.90.19224931.4931100
2.2-2.2811.80.16524601.9271100
2.28-2.38120.13324961.4251100
2.38-2.48120.10724941.4261100
2.48-2.6111.90.09425141.4591100
2.61-2.7811.80.07924911.481100
2.78-2.9911.70.07125331.4171100
2.99-3.2911.40.06425271.3071100
3.29-3.7710.90.05825541.322199.9
3.77-4.7510.30.0525781.1831100
4.75-509.80.05226751.74197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.222 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.77 / SU B: 7.387 / SU ML: 0.102 / SU R Cruickshank DPI: 0.131 / SU Rfree: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2520 5.1 %RANDOM
Rwork0.22 ---
obs0.222 49552 99.08 %-
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: 76.1 Å2 / Biso mean: 28.675 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 0 278 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223432
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.954648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73523.58176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45215585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6451529
X-RAY DIFFRACTIONr_chiral_restr0.0910.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212659
X-RAY DIFFRACTIONr_mcbond_it1.0823.52084
X-RAY DIFFRACTIONr_mcangle_it3.431503360
X-RAY DIFFRACTIONr_scbond_it7.081501348
X-RAY DIFFRACTIONr_scangle_it1.1144.51286
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 179 -
Rwork0.37 3421 -
all-3600 -
obs--99.7 %
Refinement TLS params.Method: refined / Origin x: 127.4726 Å / Origin y: 5.5108 Å / Origin z: 46.2241 Å
111213212223313233
T0.0513 Å20.0051 Å20.0038 Å2-0.0311 Å2-0.0026 Å2--0.0672 Å2
L1.2475 °2-0.3733 °20.7023 °2-0.4712 °2-0.2373 °2--0.6207 °2
S-0.0028 Å °-0.1865 Å °-0.0305 Å °-0.0499 Å °0.0287 Å °0.1147 Å °-0.0567 Å °-0.0915 Å °-0.0259 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 468
2X-RAY DIFFRACTION1A483 - 760

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