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Yorodumi- PDB-1m1a: LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m1a | |||||||||
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Title | LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / chromatin / histone / pyrrole-imidazole polyamide / DNA regognition / chromatin remodeling / STRUCTURAL PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) Synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Suto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K. | |||||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 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-IMT-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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m1a.cif.gz | 332.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m1a.ent.gz | 250.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1a ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1a | HTTPS FTP |
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-Related structure data
Related structure data | 1m18C 1m19C 1aoiS 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
-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.) Xenopus laevis (African clawed frog) / Gene: h3-5 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P02302 #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398084 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LTD2, UniProt: P62799*PLUS #4: Protein | Mass: 13962.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #5: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496, UniProt: P02281*PLUS |
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-Non-polymers , 7 types, 241 molecules
#6: Chemical | ChemComp-MN / #7: Chemical | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.86 % | |||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
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: 2.65→60 Å / Num. all: 61273 / Num. obs: 58997 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.2 |
Reflection shell | Highest resolution: 2.65 Å / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.1 / % possible all: 96.9 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. obs: 61273 / % possible obs: 99.4 % |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AOI Resolution: 2.65→60 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: 2.65→60 Å
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Refinement | *PLUS Lowest resolution: 60 Å / Rfactor Rwork: 0.223 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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