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- PDB-1bw6: HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1 -

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Basic information

Entry
Database: PDB / ID: 1bw6
TitleHUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1
ComponentsPROTEIN (CENTROMERE PROTEIN B)
KeywordsDNA BINDING PROTEIN / CENTROMERE PROTEIN / DNA-BINDING / HELIX-TURN-HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
Centromere protein B dimerisation domain / CENP-B, dimerisation domain superfamily / Major centromere autoantigen B / Centromere protein CENP-B, C-terminal domain / CENP-B N-terminal DNA-binding domain / Psq-type HTH domain profile. / DNA binding HTH domain, Psq-type / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / Tc5 transposase DNA-binding domain ...Centromere protein B dimerisation domain / CENP-B, dimerisation domain superfamily / Major centromere autoantigen B / Centromere protein CENP-B, C-terminal domain / CENP-B N-terminal DNA-binding domain / Psq-type HTH domain profile. / DNA binding HTH domain, Psq-type / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / Tc5 transposase DNA-binding domain / DDE superfamily endonuclease / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Major centromere autoantigen B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsIwahara, J. / Kigawa, T. / Kitagawa, K. / Masumoto, H. / Okazaki, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: EMBO J. / Year: 1998
Title: A helix-turn-helix structure unit in human centromere protein B (CENP-B).
Authors: Iwahara, J. / Kigawa, T. / Kitagawa, K. / Masumoto, H. / Okazaki, T. / Yokoyama, S.
History
DepositionSep 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CENTROMERE PROTEIN B)


Theoretical massNumber of molelcules
Total (without water)6,5471
Polymers6,5471
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 80
Representative

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Components

#1: Protein PROTEIN (CENTROMERE PROTEIN B)


Mass: 6546.627 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHR1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSS / References: UniProt: P07199

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: ENERGY-MINIMIZED STRUCTURE. THE STRUCTRURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CENP-B DBD RP1.

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Sample preparation

Sample conditionsIonic strength: 400 mM NA2SO4 / pH: 6.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX 500BrukerDMX 5005001
Bruker AMX 600BrukerAMX 6006002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers calculated total number: 80 / Conformers submitted total number: 1

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