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Yorodumi- PDB-1hlv: CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hlv | ||||||
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Title | CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / HELIX-TURN-HELIX / PROTEIN-DNA COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information satellite DNA binding / centromeric DNA binding / condensed chromosome, centromeric region / chromosome, centromeric region / pericentric heterochromatin / chromosome / sequence-specific DNA binding / nuclear body / chromatin binding / DNA binding ...satellite DNA binding / centromeric DNA binding / condensed chromosome, centromeric region / chromosome, centromeric region / pericentric heterochromatin / chromosome / sequence-specific DNA binding / nuclear body / chromatin binding / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Tanaka, Y. / Nureki, O. / Kurumizaka, H. / Fukai, S. / Kawaguchi, S. / Ikuta, M. / Iwahara, J. / Okazaki, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. Authors: Tanaka, Y. / Nureki, O. / Kurumizaka, H. / Fukai, S. / Kawaguchi, S. / Ikuta, M. / Iwahara, J. / Okazaki, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hlv.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hlv.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hlv_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 1hlv_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 1hlv_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 1hlv_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/1hlv ftp://data.pdbj.org/pub/pdb/validation_reports/hl/1hlv | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6494.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. |
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#2: DNA chain | Mass: 6392.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. |
#3: Protein | Mass: 15169.706 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENP-B / Plasmid: PET15D / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P07199 |
#4: 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: 4.88 Å3/Da / Density % sol: 74.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, potassium cacodylate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 10, 1999 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 19313 / Num. obs: 19313 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.9 % / Biso Wilson estimate: 58.195 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.216 / Rsym value: 0.216 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 19126 / % possible obs: 98.5 % / Num. measured all: 619774 / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 45.8703 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2253 / Rfactor Rfree: 0.2653 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å |