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- PDB-3dm7: Crystal Structure of the Vps75 Histone Chaperone -

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Basic information

Entry
Database: PDB / ID: 3dm7
TitleCrystal Structure of the Vps75 Histone Chaperone
ComponentsVacuolar protein sorting-associated protein 75
KeywordsCHAPERONE / Vps75 (vacuolar protein sorting 75) / NAP1 / histone chaperone / Nucleus / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information


H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / nucleosome assembly / protein transport / histone binding / chromatin binding / chromatin / identical protein binding ...H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / nucleosome assembly / protein transport / histone binding / chromatin binding / chromatin / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 75
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsTang, Y. / Marmorstein, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of Vps75 and implications for histone chaperone function.
Authors: Tang, Y. / Meeth, K. / Jiang, E. / Luo, C. / Marmorstein, R.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75


Theoretical massNumber of molelcules
Total (without water)55,6022
Polymers55,6022
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-27 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.010, 89.658, 94.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein 75


Mass: 27801.092 Da / Num. of mol.: 2 / Mutation: I80M, I160M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS75, YNL246W, N0890 / Plasmid: modified pRSF-GST fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P53853
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 25% PEG4000, 100 mM MES, 0.2 M malic acid, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789,0.9791,0.9537
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2007 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97911
30.95371
ReflectionResolution: 2→50 Å / Num. obs: 45182 / % possible obs: 99.1 % / Observed criterion σ(I): -3.5 / Redundancy: 13.8 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.096 / Net I/σ(I): 24.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 11 % / Mean I/σ(I) obs: 5.48 / Rsym value: 0.414 / % possible all: 95.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2259 -random
Rwork0.209 ---
obs-45182 99.1 %-
Displacement parametersBiso mean: 34.5 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 362 3800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.07

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