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Yorodumi- PDB-1per: THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1per | ||||||
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Title | THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Phage 434 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Rodgers, D.W. / Harrison, S.C. | ||||||
Citation | Journal: Structure / Year: 1993 Title: The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites. Authors: Rodgers, D.W. / Harrison, S.C. #1: Journal: J.Mol.Biol. / Year: 1993 Title: The Phage 434 OR2/R1-69 Complex at 2.5 Angstroms Resolution Authors: Shimon, L.W. / Harrison, S.C. #2: Journal: Science / Year: 1988 Title: Recognition of a DNA Operator by the Repressor of Phage 434. A View at High Resolution Authors: Aggarwal, A.K. / Rodgers, D.W. / Drottar, M. / Ptashne, M. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1per.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1per.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1per.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1per_validation.pdf.gz | 386.9 KB | Display | wwPDB validaton report |
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Full document | 1per_full_validation.pdf.gz | 398.8 KB | Display | |
Data in XML | 1per_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1per_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/1per ftp://data.pdbj.org/pub/pdb/validation_reports/pe/1per | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6128.986 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6134.031 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 7560.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phage 434 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / References: UniProt: P16117 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 8311 / % possible obs: 83.8 % / Num. measured all: 20076 / Rmerge(I) obs: 0.083 |
-Processing
Software |
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Refinement | Rfactor obs: 0.187 / Highest resolution: 2.5 Å / σ(I): 1.5 Details: THE FOLLOWING CLOSE CRYSTAL PACKING CONTACTS BETWEEN DNA CHAINS RELATED BY A TRANSLATION ALONG THE B AXIS ARE OBSERVED: C2 A 1 A - N3 T 1 B DIST= 1.68 N1 A 1 A - O4 T 1 B DIST= 1.72 N1 A 1 A ...Details: THE FOLLOWING CLOSE CRYSTAL PACKING CONTACTS BETWEEN DNA CHAINS RELATED BY A TRANSLATION ALONG THE B AXIS ARE OBSERVED: C2 A 1 A - N3 T 1 B DIST= 1.68 N1 A 1 A - O4 T 1 B DIST= 1.72 N1 A 1 A - N3 T 1 B DIST= 1.77 N1 A 1 A - C4 T 1 B DIST= 1.99 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refinement | *PLUS Highest resolution: 2.5 Å / Num. reflection obs: 7578 / σ(I): 1.5 / Rfactor obs: 0.187 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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