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Yorodumi- PDB-1b6w: CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b6w | ||||||
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Title | CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS | ||||||
Components | PROTEIN (HISTONE HMFB) | ||||||
Keywords | DNA BINDING PROTEIN / HISTONE / HMF-2 / ARCHAEAL HISTONE B | ||||||
Function / homology | Function and homology information DNA topological change / protein homooligomerization / chromosome / double-stranded DNA binding / protein heterodimerization activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Methanothermus fervidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Decanniere, K. / Sandman, K. / Reeve, J.N. / Heinemann, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 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: Journal: Proteins / Year: 1996 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: Journal: J.Mol.Biol. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b6w.cif.gz | 24.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b6w.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b6w ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b6w | HTTPS FTP |
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-Related structure data
-Links
-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.) Methanothermus fervidus (archaea) / Gene: HMFB / Production host: Escherichia coli (E. coli) / References: UniProt: P19267 |
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#2: 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: 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.877 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |