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Atomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
by single particle reconstruction, at 18 A resolution
#1: Depositted structure unit, Made by Jmol
#2: Superimposing with EM 3D map: EMDB-1534, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 2y7h |
|---|---|
| Title | Atomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534. |
| Descriptor | TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN (E.C.3.1.21.3) TYPE I RESTRICTION ENZYME ECOKI M PROTEIN (E.C.3.1.21.3 2.1.1.72) |
| Keywords |  TRANSFERASE/DNA, TRANSFERASE-DNA COMPLEX |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie Page#1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1534, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Nucleic Acids Res., Vol. 37, Page: 762 - , Year: 2009, |
|---|---|
| Title | The Structure of M.Ecoki Type I DNA Methyltransferase with a DNA Mimic Antirestriction Protein. |
| Authors | Kennaway, C.K., Obarska-Kosinska, A., White, J.H., Tuszynska, I., Cooper, L.P., Bujnicki, J.M., Trinick, J., Dryden, D.T.F. |
| Links | DOI: 10.1093/NAR/GKN988 |
 Components | |
| ID 1 : HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT, S.ECOKI, TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN, S PROTEIN | |
| Image |   |
|---|---|
| Description | TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN |
| Type | polypeptide(L) |
| Formula weight | 51468.723 Da |
| Number of molecules | 1 |
| ID | 1 |
| Ec | 3.1.21.3 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: ESCHERICHIA COLI
Strain: K |
| Links | UniProt: P05719, Sequence view |
| ID 2 : HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT, M.ECOKI | |
| Image |   |
| Description | TYPE I RESTRICTION ENZYME ECOKI M PROTEIN |
| Type | polypeptide(L) |
| Formula weight | 59378.996 Da |
| Number of molecules | 2 |
| ID | 2 |
| Ec | 3.1.21.3, 2.1.1.72 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: ESCHERICHIA COLI Strain: K |
| Links | UniProt: P08957, Sequence view |
| ID 3 : 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3' | |
| Image |   |
| Description | 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3' |
| Type | polydeoxyribonucleotide |
| Formula weight | 6119.017 Da |
| Number of molecules | 1 |
| ID | 3 |
| Details | FLIPPED OUT ADENINE |
| Source | Method: Obtained synthetically |
| Links | Sequence view |
| ID 4 : 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3' | |
| Image |   |
| Description | 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3' |
| Type | polydeoxyribonucleotide |
| Formula weight | 6150.028 Da |
| Number of molecules | 1 |
| ID | 4 |
| Details | FLIPPED OUT ADENINE BASE |
| Source | Method: Obtained synthetically |
| Links | Sequence view |
| ID 5 : S-ADENOSYLMETHIONINE | |
| Image |    |
| Description | S-ADENOSYLMETHIONINE |
| Type | non-polymer |
| Formula weight | 398.436 Da |
| Number of molecules | 2 |
| ID | 5 |
| Source | Method: Obtained synthetically |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | M.ECOKI WITH DNA |
| Buffer | |
| Name | 20MM TRIS-CL, 100 MM NACL |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | NEGATIVE STAIN |
| Sample preparation | |
| pH | 4.7 |
| Sample concentration | 0.05 mg/ml |
| Sample support | |
| Details | CARBON |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: OTHER |
|---|---|
| Date | 2008-02-01 |
| Electron gun | |
| Electron source | TUNGSTEN HAIRPIN |
| Accelerating voltage | 80 kV |
| Electron dose | 25 e/A**2 |
| Illumination mode | MEDIUM DOSE |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | Calibrated: 39500 X, Nominal: 40000 X |
| Cs | Nominal: 2 mm |
| Nominal defocus | Max: 870 nm, Min: 275 nm |
| Specimen holder | |
| Temperature | 294 Kelvin |
| Detector | |
| Type | KODAK SO163 FILM |
 Processing | |
| 2D projection selection | |
| Number of particles | 17807 |
|---|---|
| Software name | IMAGIC, EMAN, MRC,UROX,CHIMERA |
| 3D reconstruction | |
| Actual pixel size | 3.12 A/pix |
| CTF correction method | FILTERED AT FIRST ZERO |
| Details | HSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY. |
| Magnification calibration | TMV |
| Method | RANDOM SPHERES STARTING MODEL |
| Nominal pixel size | 3.12 A/pix |
| Resolution | 18 A |
| 3D fitting | |
| Method | UROX |
| Refinement Protocol | RIGID BODY |
| Refinement Space | REAL |
| 3D fitting list | |
| 3D fitting id | 1 |
| PDB entry ID | 1S7Z, 1YF2, 2AR0 |
| Refine | |
| Refine id | ELECTRON MICROSCOPY |
| Ls d res high | 18.00 A |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| D res high | 18.00 |
| Total atoms | 12846 |
| Ligand atoms | 54 |
| Nucleic acid atoms | 820 |
| Protein atoms | 11972 |
 Download | |||
| PDB format | |||
| All | pdb2y7h.ent.gzpdb2y7h.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb2y7h.ent.gz | ||
| mmCIF format | |||
| mmCIF | 2y7h.cif.gz | ||
| XML format | |||
| All | 2y7h.xml.gz | ||
| No-atom | 2y7h-noatom.xml.gz | ||
| Ext-atom | 2y7h-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
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