+Open data
-Basic information
Entry | Database: PDB / ID: 7mht | ||||||
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Title | CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE / METHYLTRANSFERASE / RESTRICTION SYSTEM / COMPLEX (METHYLTRANSFERASE- DNA) / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.87 Å | ||||||
Authors | O'Gara, M. / Horton, J.R. / Roberts, R.J. / Cheng, X. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Authors: O'Gara, M. / Horton, J.R. / Roberts, R.J. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mht.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mht.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/7mht ftp://data.pdbj.org/pub/pdb/validation_reports/mh/7mht | HTTPS FTP |
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-Related structure data
Related structure data | 8mhtC 9mhtC 5mhtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3703.416 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 37042.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05102, EC: 2.1.1.73 |
#4: Chemical | ChemComp-SAH / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: 1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7.25 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→23 Å / Num. obs: 13031 / % possible obs: 90 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.3 |
Reflection | *PLUS % possible obs: 90 % / Observed criterion σ(I): 2 / Num. measured all: 55718 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 5MHT Resolution: 2.87→23 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.87→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.87→3 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 23 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.199 / Rfactor obs: 0.199 |