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Yorodumi- PDB-1lwm: Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lwm | ||||||
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Title | Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A | ||||||
Components | NONHISTONE CHROMOSOMAL PROTEIN 6A | ||||||
Keywords | DNA BINDING PROTEIN / HMG-BOX / HMGB / ALPHA HELIX | ||||||
Function / homology | Function and homology information maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / RNA polymerase III preinitiation complex assembly / DNA binding, bending / negative regulation of DNA binding / nucleosome binding / RNA polymerase II preinitiation complex assembly / protein-DNA complex ...maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / RNA polymerase III preinitiation complex assembly / DNA binding, bending / negative regulation of DNA binding / nucleosome binding / RNA polymerase II preinitiation complex assembly / protein-DNA complex / chromosome / chromatin organization / nucleic acid binding / chromatin remodeling / DNA repair / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding Authors: Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lwm.cif.gz | 594.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lwm.ent.gz | 517.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lwm ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lwm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10824.364 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NHP6A / Production host: Escherichia coli (E. coli) / References: UniProt: P11632 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure calculated using the same data as previously used in the 1999 structure 1CG7 but using new a-helix hydrogen bond restraints and XPLOR instead of DYANA. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 10 mM NaPO4, 100 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 293 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on the same restraints as previously used in the 1999 structure 1CG7, but different a-helix hydrogen bond restraints were included. These are the same as those used ...Details: The structures are based on the same restraints as previously used in the 1999 structure 1CG7, but different a-helix hydrogen bond restraints were included. These are the same as those used to calculate the structure of the complex with SRY_DNA. | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average,lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |