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- PDB-2ayu: The structure of nucleosome assembly protein suggests a mechanism... -

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Basic information

Entry
Database: PDB / ID: 2ayu
TitleThe structure of nucleosome assembly protein suggests a mechanism for histone binding and shuttling
ComponentsNucleosome assembly protein
KeywordsCHAPERONE / Nucleosome assembly protein 1 (NAP1) / Histone chaperone
Function / homology
Function and homology information


protein localization to cell division site after cytokinesis / cellular bud neck septin collar / Gin4 complex / budding cell bud growth / septin ring assembly / septum digestion after cytokinesis / NLS-bearing protein import into nucleus / nucleosome disassembly / cell division site / positive regulation of microtubule polymerization ...protein localization to cell division site after cytokinesis / cellular bud neck septin collar / Gin4 complex / budding cell bud growth / septin ring assembly / septum digestion after cytokinesis / NLS-bearing protein import into nucleus / nucleosome disassembly / cell division site / positive regulation of microtubule polymerization / cyclin binding / enzyme activator activity / positive regulation of transcription elongation by RNA polymerase II / unfolded protein binding / nucleosome assembly / ribosomal small subunit biogenesis / histone binding / chromatin binding / chromatin / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Nucleosome assembly protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsPark, Y.J. / Luger, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The structure of nucleosome assembly protein 1.
Authors: Park, Y.J. / Luger, K.
History
DepositionSep 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome assembly protein


Theoretical massNumber of molelcules
Total (without water)47,9301
Polymers47,9301
Non-polymers00
Water00
1
A: Nucleosome assembly protein

A: Nucleosome assembly protein


Theoretical massNumber of molelcules
Total (without water)95,8612
Polymers95,8612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area8130 Å2
ΔGint-68 kcal/mol
Surface area28820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.7, 86.7, 176.1
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Nucleosome assembly protein


Mass: 47930.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NAP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P25293
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: mono-ammonium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.111.1
SYNCHROTRONALS 5.0.120.9796, 0.9795, 0.9642
Detector
IDDetector
1CCD
2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97961
30.97951
40.96421
ReflectionResolution: 3→50 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.25 / σ(F): 0 / σ(I): 0
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 0 0 2323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.08892
X-RAY DIFFRACTIONc_angle_deg1.44295

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