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- PDB-6abs: Actin interacting protein 5 (Aip5, mutant) -

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Basic information

Entry
Database: PDB / ID: 6abs
TitleActin interacting protein 5 (Aip5, mutant)
ComponentsActin binding protein
KeywordsSTRUCTURAL PROTEIN / Actin binding protein
Function / homologycellular bud / Glutaredoxin domain profile. / Thioredoxin-like superfamily / cytoplasm / TRIETHYLENE GLYCOL / Uncharacterized protein YFR016C
Function and homology information
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSun, J. / Ying, X. / Toh, J. / Hong, W. / Miao, Y. / Gao, Y.G.
CitationJournal: Nat Commun / Year: 2019
Title: Polarisome scaffolder Spa2-mediated macromolecular condensation of Aip5 for actin polymerization.
Authors: Xie, Y. / Sun, J. / Han, X. / Tursic-Wunder, A. / Toh, J.D.W. / Hong, W. / Gao, Y.G. / Miao, Y.
History
DepositionJul 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Actin binding protein
B: Actin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8164
Polymers28,4282
Non-polymers3882
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-1 kcal/mol
Surface area10940 Å2
Unit cell
Length a, b, c (Å)38.942, 54.596, 128.652
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 Actin binding protein


Mass: 14213.838 Da / Num. of mol.: 2 / Fragment: UNP residues 1110-1233 / Mutation: L1150A, N1162A, S1165C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: YFR016C / Production host: Escherichia coli (E. coli) / References: UniProt: P43597
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium phosphate citrate pH 4.2, 40% PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14417 / % possible obs: 98.3 % / Redundancy: 4.9 % / Rsym value: 0.111 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 699 / Rsym value: 0.639

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ABR

6abr


Resolution: 2.2→37.272 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2465 1418 10 %
Rwork0.1974 --
obs0.2023 14179 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 26 87 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081662
X-RAY DIFFRACTIONf_angle_d1.1192234
X-RAY DIFFRACTIONf_dihedral_angle_d14.862642
X-RAY DIFFRACTIONf_chiral_restr0.04243
X-RAY DIFFRACTIONf_plane_restr0.004281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1967-2.27520.27071350.21421141X-RAY DIFFRACTION89
2.2752-2.36630.24421430.20271200X-RAY DIFFRACTION95
2.3663-2.4740.26361380.19791263X-RAY DIFFRACTION97
2.474-2.60440.25511360.19351288X-RAY DIFFRACTION99
2.6044-2.76750.24111300.19551310X-RAY DIFFRACTION100
2.7675-2.98110.26561600.19471277X-RAY DIFFRACTION99
2.9811-3.2810.24421550.19751295X-RAY DIFFRACTION100
3.281-3.75530.1991290.18681287X-RAY DIFFRACTION97
3.7553-4.72980.23181340.17421295X-RAY DIFFRACTION95
4.7298-37.27730.28071580.22851405X-RAY DIFFRACTION98

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