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Yorodumi- PDB-1mus: crystal structure of Tn5 transposase complexed with resolved outs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mus | ||||||
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Title | crystal structure of Tn5 transposase complexed with resolved outside end DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / transposase / hairpin / dna binding / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information transposase activity / DNA transposition / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. / Steiniger-White, M. / Reznikoff, W.S. / Lovell, S. / Rayment, I. | ||||||
Citation | Journal: Curr.Opin.Struct.Biol. / Year: 2004 Title: Structure/function insights into Tn5 transposition. Authors: Steiniger-White, M. / Rayment, I. / Reznikoff, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mus.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mus.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mus_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 1mus_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 1mus_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 1mus_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/1mus ftp://data.pdbj.org/pub/pdb/validation_reports/mu/1mus | HTTPS FTP |
-Related structure data
Related structure data | 1f3i S: Starting model for refinement |
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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 on special symmetry positions |
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Details | homodimer, the other half of the dimer may be generated by use of the following rotation matrix and translation vector ROTATION MATRIX: 0.50000 0.86603 0.00000 0.86603 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS -0.00045 -0.00055 196.58308 |
-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 6213.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON |
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#2: DNA chain | Mass: 6052.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 53323.102 Da / Num. of mol.: 1 / Mutation: E54K, M56A, D119K, K120A, E345K, L372P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)pLysS / References: UniProt: Q46731 |
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-Non-polymers , 4 types, 622 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: batch / pH: 7.5 Details: PEG-1500, Hepes, manganese chloride, magnesium chloride, pH 7.5, batch, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.7 / Method: batch method / Details: Davies, D.R., (2000) Science, 289, 77. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 61106 / Num. obs: 61106 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.063 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 4221 / Rsym value: 0.224 / % possible all: 61.2 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F3I 1f3i Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |