+Open data
-Basic information
Entry | Database: PDB / ID: 8mht | ||||||
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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 / methylation / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.76 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 | 8mht.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8mht.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 8mht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8mht_validation.pdf.gz | 462.3 KB | Display | wwPDB validaton report |
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Full document | 8mht_full_validation.pdf.gz | 489.8 KB | Display | |
Data in XML | 8mht_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 8mht_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/8mht ftp://data.pdbj.org/pub/pdb/validation_reports/mh/8mht | HTTPS FTP |
-Related structure data
Related structure data | 7mhtC 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: 3624.353 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: 3.49 Å3/Da / Density % sol: 64.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: 1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknown / pH: 7.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.76→23.1 Å / Num. obs: 13839 / % possible obs: 85.2 % / Redundancy: 3.09 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.2 |
Reflection | *PLUS Num. measured all: 42797 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 5MHT Resolution: 2.76→23.1 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.76→23.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.89 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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