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- PDB-3c9d: Crystal structure of Vps75 -

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Basic information

Entry
Database: PDB / ID: 3c9d
TitleCrystal structure of Vps75
ComponentsVacuolar protein sorting-associated protein 75
KeywordsCHAPERONE / chromatin / 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 / Resolution: 2 Å
AuthorsBerndsen, C.E. / Tsubota, T. / Lindner, S.E. / Lee, S. / Holton, J.M. / Kaufman, P.D. / Keck, J.L. / Denu, J.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75
Authors: Berndsen, C.E. / Tsubota, T. / Lindner, S.E. / Lee, S. / Holton, J.M. / Kaufman, P.D. / Keck, J.L. / Denu, J.M.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75


Theoretical massNumber of molelcules
Total (without water)60,0242
Polymers60,0242
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-32 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.805, 86.085, 85.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein 75


Mass: 30012.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS75 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P53853
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Tris, 100 mM KCl, 10 mM MgCl(2), 35% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37867 / Num. obs: 37640 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Χ2: 1.335 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.408 / Num. unique all: 3590 / Χ2: 1.015 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
PHASERphasing
RefinementResolution: 2→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.089 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1866 5 %RANDOM
Rwork0.229 ---
all0.23 37839 --
obs0.23 37548 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.32 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2---0.59 Å20 Å2
3----2.84 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 0 309 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223546
X-RAY DIFFRACTIONr_angle_refined_deg0.8441.9484775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88224.144181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06815647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4251518
X-RAY DIFFRACTIONr_chiral_restr0.0620.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022702
X-RAY DIFFRACTIONr_nbd_refined0.2280.21659
X-RAY DIFFRACTIONr_nbtor_refined0.310.22410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3690.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3810.240
X-RAY DIFFRACTIONr_mcbond_it0.6651.52122
X-RAY DIFFRACTIONr_mcangle_it1.07623330
X-RAY DIFFRACTIONr_scbond_it1.71131655
X-RAY DIFFRACTIONr_scangle_it2.8624.51445
LS refinement shellResolution: 2.003→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 120 -
Rwork0.257 2398 -
all-2518 -
obs--92.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5597-0.14190.01070.69120.22270.77370.07590.07560.0742-0.03230.0643-0.1357-0.01780.113-0.14020.00640.02290.0064-0.0331-0.0164-0.0463-0.89010.6554-8.4571
20.7117-0.5302-0.29870.95040.11310.58830.01320.0173-0.1048-0.06760.01790.07580.03-0.035-0.0311-0.0762-0.0098-0.012-0.07410.0048-0.039-8.1002-15.293418.7161
30.2887-0.1425-0.11140.1716-0.07410.20740.03710.0045-0.01730.0090.0080.0322-0.00270.0222-0.0451-0.0212-0.0027-0.0084-0.0262-0.00540.0308-4.9392-8.82517.9136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 221
2X-RAY DIFFRACTION2B11 - 221
3X-RAY DIFFRACTION3A260 - 394

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