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- PDB-7c03: Crystal structure of POLArISact(T57S), genetically encoded probe ... -

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Basic information

Entry
Database: PDB / ID: 7c03
TitleCrystal structure of POLArISact(T57S), genetically encoded probe for fluorescent polarization
ComponentsPOLArISact(T57S)
KeywordsLUMINESCENT PROTEIN / Fluorescent protein Fluorescent polarization Protein engineering
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å
AuthorsTomabechi, Y. / Sakai, N. / Shirouzu, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos.
Authors: Sugizaki, A. / Sato, K. / Chiba, K. / Saito, K. / Kawagishi, M. / Tomabechi, Y. / Mehta, S.B. / Ishii, H. / Sakai, N. / Shirouzu, M. / Tani, T. / Terada, S.
History
DepositionApr 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLArISact(T57S)


Theoretical massNumber of molelcules
Total (without water)39,0811
Polymers39,0811
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16200 Å2
2
A: POLArISact(T57S)

A: POLArISact(T57S)


Theoretical massNumber of molelcules
Total (without water)78,1622
Polymers78,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area3170 Å2
ΔGint-18 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.130, 113.590, 132.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein POLArISact(T57S)


Mass: 39081.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.76 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate (pH4.5-5.0), 6-8% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20785 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.912 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 45440 / CC1/2: 0.644

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.31 Å46.2 Å
Translation6.31 Å46.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EVP

3evp


Resolution: 2.501→46.202 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1999 9.62 %
Rwork0.2141 18786 -
obs0.2165 20785 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.21 Å2 / Biso mean: 89.6744 Å2 / Biso min: 42.09 Å2
Refinement stepCycle: final / Resolution: 2.501→46.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 81 2609
Biso mean---73.48 -
Num. residues----313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.501-2.56350.43251400.43191319145999
2.5635-2.63280.46561390.381913081447100
2.6328-2.71030.35721420.336613401482100
2.7103-2.79770.34161400.290113201460100
2.7977-2.89770.29931420.276613281470100
2.8977-3.01370.28651420.254513271469100
3.0137-3.15080.25081390.235113171456100
3.1508-3.31690.26431410.219413271468100
3.3169-3.52470.22771440.209413521496100
3.5247-3.79670.21751420.213413311473100
3.7967-4.17850.25711450.203413571502100
4.1785-4.78270.22251440.163813521496100
4.7827-6.02350.19981470.184813751522100
6.0235-46.20940.20121520.216214331585100

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