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- PDB-1m19: LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m19 | |||||||||
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Title | LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA | |||||||||
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![]() | STRUCTURAL PROTEIN/DNA / nucleosome / chromatin / histone / pyrrole-imidazole polyamide / DNA regognition / chromatin remodeling / STRUCTURAL PROTEIN-DNA COMPLEX | |||||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() Synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Suto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K. | |||||||||
![]() | ![]() Title: Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands Authors: Suto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K. | |||||||||
History |
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Remark 600 | HETEROGEN THE PYRROLE-IMIDAZOLE POLYAMIDE CONSISTS OF THE FOLLOWING GROUPS LINKED BY PEPTIDE BONDS. ...HETEROGEN THE PYRROLE-IMIDAZOLE POLYAMIDE CONSISTS OF THE FOLLOWING GROUPS LINKED BY PEPTIDE BONDS. IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB IMT = 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID PYB = 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID ABU = GAMMA-AMINO-BUTANOIC ACID; GAMMA(AMINO)-BUTYRIC ACID BAL = BETA-ALANINE DIB = 3-AMINO-(DIMETHYLPROPYLAMINE) | |||||||||
Remark 999 | SEQUENCE AUTHOR INDICATES ARG-SER DISCREPANCY AT RESIDUE 86 IS A CONFLICT BETWEEN SEQUENCE AND ...SEQUENCE AUTHOR INDICATES ARG-SER DISCREPANCY AT RESIDUE 86 IS A CONFLICT BETWEEN SEQUENCE AND SEQUENCE DATABASE REFERENCE SWISSPROT ENTRY P02302. SER WAS CRYSTALLIZED AT POSITION 486,686 FOR CHAINS A,E. AUTHOR INFORMS GLY-ARG MISMATCH AT RESIDUE 899,1099 (CHAINS C,G) AND SER-THR MISMATCH AT RESIDUE 1229,1429 (CHAINS D,H) ARE VARIANTS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357 KB | Display | ![]() |
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PDB format | ![]() | 270.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.1 KB | Display | ![]() |
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Full document | ![]() | 574.1 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 45.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m18C ![]() 1m1aC ![]() 1aoiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15320.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13962.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 723 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/IMT.gif)
![](data/chem/img/PYB.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/BAL.gif)
![](data/chem/img/DIB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMT.gif)
![](data/chem/img/PYB.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/BAL.gif)
![](data/chem/img/DIB.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-IMT / #8: Chemical | ChemComp-PYB / #9: Chemical | ChemComp-ABU / #10: Chemical | ChemComp-BAL / #11: Chemical | ChemComp-DIB / #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: used macroseeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→80 Å / Num. all: 96437 / Num. obs: 93443 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.4 |
Reflection shell | Highest resolution: 2.3 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.2 / % possible all: 93.6 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 80 Å / % possible obs: 99 % |
Reflection shell | *PLUS % possible obs: 93.6 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AOI Resolution: 2.3→80 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→80 Å
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 80 Å / Num. reflection all: 96437 / Num. reflection obs: 93612 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.214 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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