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- PDB-1b6w: CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b6w | ||||||
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Title | CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS | ||||||
![]() | PROTEIN (HISTONE HMFB) | ||||||
![]() | DNA BINDING PROTEIN / HISTONE / HMF-2 / ARCHAEAL HISTONE B | ||||||
Function / homology | ![]() DNA topological change / protein homooligomerization / chromosome / double-stranded DNA binding / protein heterodimerization activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Decanniere, K. / Sandman, K. / Reeve, J.N. / Heinemann, U. | ||||||
![]() | ![]() Title: Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus. Authors: Decanniere, K. / Babu, A.M. / Sandman, K. / Reeve, J.N. / Heinemann, U. #1: ![]() Title: Crystallization and Preliminary X-Ray Characterization of the Methanothermus Fervidus Histones Hmfa and Hmfb Authors: Decanniere, K. / Sandman, K. / Reeve, J.N. / Heinemann, U. #2: ![]() Title: NMR Structure of Hmfb from the Hyperthermophyle, Methanothermus Fervidus, Confirms that This Archaeal Protein is a Histone Authors: Starich, M.R. / Sandman, K. / Reeve, J.N. / Summers, M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.2 KB | Display | ![]() |
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PDB format | ![]() | 15.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399 KB | Display | ![]() |
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Full document | ![]() | 399.2 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 7776.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THIS IS A SELENOMETHIONINE PROTEIN. RESIDUES 1 AND 35 ARE SEMET (BUT SIDE CHAIN OF RESIDUE 1 IS DISORDERED) Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % Description: ORTHOROMBIC HMFA STRUCTURE WILL BE SUBMITTED SOON | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: IMAGE PLATE 18 CM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.877 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→14 Å / Num. obs: 11343 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 8.8 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.2 / Rsym value: 20 / % possible all: 65.8 |
Reflection | *PLUS Highest resolution: 2.05 Å / % possible obs: 97.2 % / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / % possible obs: 90.2 % / Rmerge(I) obs: 0.158 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PARTIALLY REFINED ORTHORHOMBIC HMFA Resolution: 2.05→18 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.05→18 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |