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- PDB-7vf4: Crystal structure of Vps75 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7vf4
TitleCrystal structure of Vps75 from Candida albicans
ComponentsVps75
KeywordsCHAPERONE / Candida albicans / Vps75 / Histone Chaperon / histone lysine acetylation / Rtt109
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 / 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 speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, W. / Chen, X. / Yang, Z. / Chen, X. / Li, C. / Wang, M.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2108085MC75 China
Other government1808085MC53 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of histone chaperone Vps75 from Candida albicans.
Authors: Wang, W. / Chen, X. / Yang, Z. / Chen, X. / Li, C. / Wang, M.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vps75
B: Vps75
C: Vps75
D: Vps75
E: Vps75
F: Vps75
G: Vps75
H: Vps75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,70120
Polymers224,3768
Non-polymers32612
Water36020
1
A: Vps75
B: Vps75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2347
Polymers56,0942
Non-polymers1405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-71 kcal/mol
Surface area25340 Å2
MethodPISA
2
C: Vps75
D: Vps75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1404
Polymers56,0942
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-53 kcal/mol
Surface area25320 Å2
MethodPISA
3
E: Vps75
F: Vps75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1885
Polymers56,0942
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-41 kcal/mol
Surface area25110 Å2
MethodPISA
4
G: Vps75
H: Vps75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1404
Polymers56,0942
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-40 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.610, 137.170, 226.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 160 or resid 167 through 225))
21(chain B and (resid 8 through 160 or resid 167 through 225))
31(chain C and (resid 8 through 160 or resid 167 through 225))
41(chain D and (resid 8 through 160 or resid 167 through 225))
51(chain E and (resid 8 through 160 or resid 167 through 225))
61(chain F and resid 8 through 225)
71(chain G and (resid 8 through 160 or resid 167 through 225))
81(chain H and resid 8 through 225)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTYRTYR(chain A and (resid 8 through 160 or resid 167 through 225))AA8 - 1609 - 161
12ASPASPSERSER(chain A and (resid 8 through 160 or resid 167 through 225))AA167 - 225168 - 226
21LYSLYSTYRTYR(chain B and (resid 8 through 160 or resid 167 through 225))BB8 - 1609 - 161
22ASPASPSERSER(chain B and (resid 8 through 160 or resid 167 through 225))BB167 - 225168 - 226
31LYSLYSTYRTYR(chain C and (resid 8 through 160 or resid 167 through 225))CC8 - 1609 - 161
32ASPASPSERSER(chain C and (resid 8 through 160 or resid 167 through 225))CC167 - 225168 - 226
41LYSLYSTYRTYR(chain D and (resid 8 through 160 or resid 167 through 225))DD8 - 1609 - 161
42ASPASPSERSER(chain D and (resid 8 through 160 or resid 167 through 225))DD167 - 225168 - 226
51LYSLYSTYRTYR(chain E and (resid 8 through 160 or resid 167 through 225))EE8 - 1609 - 161
52ASPASPSERSER(chain E and (resid 8 through 160 or resid 167 through 225))EE167 - 225168 - 226
61LYSLYSSERSER(chain F and resid 8 through 225)FF8 - 2259 - 226
71LYSLYSTYRTYR(chain G and (resid 8 through 160 or resid 167 through 225))GG8 - 1609 - 161
72ASPASPSERSER(chain G and (resid 8 through 160 or resid 167 through 225))GG167 - 225168 - 226
81LYSLYSSERSER(chain H and resid 8 through 225)HH8 - 2259 - 226

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Components

#1: Protein
Vps75


Mass: 28046.943 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Gene: CAALFM_CR05890CA, orf19.6625 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D8PT39
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M cesium chloride, 0.1M MES monohydrate pH 6.5, 30% (v/v) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 47803 / % possible obs: 99.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Χ2: 0.953 / Net I/σ(I): 5.6 / Num. measured all: 613898
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.2112.71.36546650.8020.3941.4220.89598.8
3.21-3.3413.60.8747140.9210.2420.9040.90799.1
3.34-3.4913.50.54847050.9660.1530.5690.91399.2
3.49-3.6813.50.38547220.9780.1080.40.92799.3
3.68-3.9113.10.25547310.9870.0730.2650.9599.2
3.91-4.21120.16647640.9940.050.1740.98999.2
4.21-4.6313.50.12547900.9960.0350.130.98199.3
4.63-5.3130.10447940.9960.030.1081.00599.4
5.3-6.67120.09148590.9970.0270.0951.00699.5
6.67-5011.60.05650590.9990.0170.0590.96498.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q66

3q66


Resolution: 3.1→37.75 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2922 2419 5.09 %
Rwork0.2445 45144 -
obs0.2468 47563 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.77 Å2 / Biso mean: 76.2979 Å2 / Biso min: 22.9 Å2
Refinement stepCycle: final / Resolution: 3.1→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14683 0 12 20 14715
Biso mean--60.62 48.63 -
Num. residues----1750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8674X-RAY DIFFRACTION11.624TORSIONAL
12B8674X-RAY DIFFRACTION11.624TORSIONAL
13C8674X-RAY DIFFRACTION11.624TORSIONAL
14D8674X-RAY DIFFRACTION11.624TORSIONAL
15E8674X-RAY DIFFRACTION11.624TORSIONAL
16F8674X-RAY DIFFRACTION11.624TORSIONAL
17G8674X-RAY DIFFRACTION11.624TORSIONAL
18H8674X-RAY DIFFRACTION11.624TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.160.4491360.39112545268198
3.16-3.230.41021390.34562661280099
3.23-3.310.35291420.32352616275899
3.31-3.390.3441380.31412621275999
3.39-3.480.35271520.28552650280299
3.48-3.580.34121190.28082624274399
3.58-3.70.29881360.27082637277399
3.7-3.830.31551490.25722660280999
3.83-3.980.26131450.25382634277999
3.98-4.170.32061670.23842621278899
4.17-4.390.27491290.22232658278799
4.39-4.660.28191470.21152667281499
4.66-5.020.25771570.21322676283399
5.02-5.520.27461450.2112690283599
5.52-6.320.29881540.22832682283699
6.32-7.940.29971380.24952740287899
7.95-37.750.22221260.21162762288895

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