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- PDB-5agc: Crystallographic forms of the Vps75 tetramer -

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Basic information

Entry
Database: PDB / ID: 5agc
TitleCrystallographic forms of the Vps75 tetramer
ComponentsVACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75Vacuole
KeywordsTRANSPORT PROTEIN / VPS75 / VACUOLAR PROTEIN SORTING 75 / HISTONE CHAPERONE / NAP1 / CHROMATIN
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 / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsHammond, C.M. / Sundaramoorthy, R. / Owen-Hughes, T.
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: The Histone Chaperone Vps75 Forms Multiple Oligomeric Assemblies Capable of Mediating Exchange between Histone H3-H4 Tetramers and Asf1-H3-H4 Complexes.
Authors: Hammond, C.M. / Sundaramoorthy, R. / Larance, M. / Lamond, A. / Stevens, M.A. / El-Mkami, H. / Norman, D.G. / Owen-Hughes, T.
#1: Journal: Nucleic Acids Res. / Year: 2014
Title: The Histone Chaperones Vps75 and Nap1 Form Ring-Like, Tetrameric Structures in Solution.
Authors: Bowman, A. / Hammond, C.M. / Stirling, A. / Ward, R. / Shang, W. / El-Mkami, H. / Robinson, D.A. / Svergun, D.I. / Norman, D.G. / Owen-Hughes, T.
History
DepositionJan 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
1
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
3
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Unit cell
Length a, b, c (Å)82.750, 92.430, 160.750
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1485, -0.9667, 0.2084), (-0.9587, 0.0891, -0.27), (0.2424, -0.2399, -0.9401)-6.174, 3.872, 84.08
2given(-0.8552, -0.05984, -0.5147), (0.05607, -0.9982, 0.02289), (-0.5152, 0.009284, -0.857)-37.11, 13.24, -10.8
3given(0.149, 0.9583, 0.2439), (0.9586, -0.07943, -0.2736), (-0.2428, 0.2745, -0.9304)-28.04, 8.78, 76.43

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Components

#1: Protein
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75 / Vacuole


Mass: 30656.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: P53853

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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: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M SODIUM CACODYLATE PH 6.5, 25% W/V PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4→50.06 Å / Num. obs: 9771 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7
Reflection shellResolution: 4→4.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZD7

2zd7


Resolution: 4→50.06 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.915 / SU B: 63.669 / SU ML: 0.829 / Cross valid method: THROUGHOUT / ESU R Free: 0.93 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26463 495 4.8 %RANDOM
Rwork0.22934 ---
obs0.23104 9771 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 4→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7250 0 0 0 7250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197442
X-RAY DIFFRACTIONr_bond_other_d0.0070.025268
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9510025
X-RAY DIFFRACTIONr_angle_other_deg1.17312792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7195865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09924.606393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.752151363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1451536
X-RAY DIFFRACTIONr_chiral_restr0.0870.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218203
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 42 -
Rwork0.389 657 -
obs--95.36 %

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