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Yorodumi- PDB-1nhh: Crystal structure of N-terminal 40KD MutL protein (LN40) complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nhh | ||||||
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Title | Crystal structure of N-terminal 40KD MutL protein (LN40) complex with ADPnP and one Rubidium | ||||||
Components | DNA mismatch repair protein mutL | ||||||
Keywords | REPLICATION / SIGNALING PROTEIN / DNA mismatch repair / MutL / ATPase / Rubidium | ||||||
Function / homology | Function and homology information single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hu, X. / Machius, M. / Yang, W. | ||||||
Citation | Journal: FEBS Lett. / Year: 2003 Title: Monovalent cation dependence and preference of GHKL ATPases and kinases Authors: Hu, X. / Machius, M. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nhh.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nhh.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nhh ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nhh | HTTPS FTP |
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-Related structure data
Related structure data | 1nhiC 1nhjC 1b63S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37215.348 Da / Num. of mol.: 1 / Fragment: N-terminal 40KD ATPase fragment (LN40) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: mutL / Plasmid: pET15b pTX418 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: Q8XDN4, UniProt: P23367*PLUS |
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-Non-polymers , 5 types, 206 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-RB / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ANP / | #6: 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: 2.6 Å3/Da / Density % sol: 52.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: evaporation, recrystallization / pH: 8.4 Details: PEG 4000, lithium choloride, potassium choloride, megnesium choloride, DTT, EDTA, pH 8.4, EVAPORATION, RECRYSTALLIZATION, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop / Details: Ban, C., (1999) Cell(Cambridge,Mass.), 97, 85. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 5, 2002 / Details: mirrors |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 31540 / Num. obs: 29493 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 71.5 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 93.3 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 92.1 % / Rmerge(I) obs: 0.286 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B63 Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.202 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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