- PDB-1lwm: Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1lwm
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 / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / Pyroptosis / RNA polymerase III preinitiation complex assembly / Mitochondrial protein degradation / DNA binding, bending ...maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / Pyroptosis / RNA polymerase III preinitiation complex assembly / Mitochondrial protein degradation / DNA binding, bending / negative regulation of DNA binding / nucleosome binding / RNA polymerase II preinitiation complex assembly / Neutrophil degranulation / protein-DNA complex / chromatin organization / chromosome / nucleic acid binding / chromatin remodeling / DNA repair / nucleus Similarity search - Function
High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
structures with acceptable covalent geometry,structures with the lowest energy
Representative
Model #1
closest to the average,lowest energy
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Components
#1: Protein
NONHISTONECHROMOSOMALPROTEIN6A / NHP6A
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
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 15N-separated NOESY
1
2
2
3D 13C-separated NOESY
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.
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 2mM 15N-labeled NHP6A
90% H2O, 10% D2Oor100% D2O
2
2mM 13C/15N-labeled NHP6A
90% H2O, 10% D2Oor100% D2O
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
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
2.6
Bruker
collection
XwinNMR
2.6
Bruker
processing
Felix
2000
MSI
dataanalysis
X-PLOR
3.1
Brunger
structuresolution
X-PLOR
3.1
Brunger
refinement
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
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