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- PDB-2y7h: Atomic model of the DNA-bound methylase complex from the Type I r... -

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Basic information

Entry
Database: PDB / ID: 2y7h
TitleAtomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
DescriptorTYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (18 Å resolution / Particle / Single particle)
AuthorsKennaway, C.K. / Obarska-Kosinska, A. / White, J.H. / Tuszynska, I. / Cooper, L.P. / Bujnicki, J.M. / Trinick, J. / Dryden, D.T.F.
CitationNucleic Acids Res., 2009, 37, 762-770

Nucleic Acids Res., 2009, 37, 762-770 Yorodumi Papers
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
Christopher K Kennaway / Agnieszka Obarska-Kosinska / John H White / Irina Tuszynska / Laurie P Cooper / Janusz M Bujnicki / John Trinick / David T F Dryden

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 31, 2011 / Release: Feb 9, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 9, 2011Structure modelrepositoryInitial release
1.1Mar 20, 2013Structure modelOther / Refinement description / Version format compliance
1.2Aug 23, 2017Structure modelData collection / Derived calculationsem_image_scans / em_software / struct_conn_em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Assembly

Deposited unit
A: TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
B: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
C: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
D: 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'
E: 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2917
Polyers182,4945
Non-polymers7972
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT / S.ECOKI / TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / S PROTEIN


Mass: 51468.191 Da / Num. of mol.: 1
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P05719, EC: 3.1.21.3

Molecular function

Biological process

#2: Polypeptide(L)TYPE I RESTRICTION ENZYME ECOKI M PROTEIN / HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT / M.ECOKI


Mass: 59378.324 Da / Num. of mol.: 2
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P08957, EC: 3.1.21.3, EC: 2.1.1.72

Cellular component

Molecular function

Biological process

#3: DNA chain5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'


Mass: 6118.968 Da / Num. of mol.: 1 / Details: FLIPPED OUT ADENINE
Source: (synth.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
#4: DNA chain5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'


Mass: 6149.978 Da / Num. of mol.: 1 / Details: FLIPPED OUT ADENINE BASE
Source: (synth.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
#5: ChemicalChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Formula: C15H22N6O5S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: M.ECOKI WITH DNA / Type: COMPLEX
Buffer solutionName: 20MM TRIS-CL, 100 MM NACL / Details: 20MM TRIS-CL, 100 MM NACL / pH: 4.7
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 1200EX / Date: Feb 1, 2008
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 / Calibrated magnification: 39500 / Nominal defocus max: 870 nm / Nominal defocus min: 275 nm / Cs: 2 mm
Specimen holderTemperature: 294 kelvins
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1SitusMODEL FITTING1
2UCSF ChimeraMODEL FITTING1
3UROMODEL FITTING1
4EMANRECONSTRUCTION1
5IMAGICRECONSTRUCTION1
6MRC IMAGE PROCESSING PACKAGERECONSTRUCTION1
CTF correctionDetails: FILTERED AT FIRST ZERO
SymmetryPoint symmetry: C2
3D reconstructionMethod: RANDOM SPHERES STARTING MODEL / Resolution: 18 Å / Number of particles: 17807 / Nominal pixel size: 3.12 / Actual pixel size: 3.12 / Magnification calibration: TMV
Details: HSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--UROX REFINEMENT PROTOCOL--RIGID BODY / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11S7Z1
21YF21
32AR01
Least-squares processHighest resolution: 18 Å
Refine hist #LASTHighest resolution: 18 Å
Number of atoms included #LASTProtein: 11972 / Nucleic acid: 820 / Ligand: 54 / Solvent: 0 / Total: 12846

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