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- PDB-6iqf: crystal structure of Arabidopsis thaliana Profilin 3 -

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Basic information

Entry
Database: PDB / ID: 6iqf
Titlecrystal structure of Arabidopsis thaliana Profilin 3
ComponentsPRF3
KeywordsPLANT PROTEIN / actin binding / regulate actin network
Function / homology
Function and homology information


actin monomer binding / defense response / cell cortex / cytoskeleton
Similarity search - Function
Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.457 Å
AuthorsQiao, Z. / Gao, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural and computational examination of theArabidopsisprofilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly.
Authors: Qiao, Z. / Sun, H. / Ng, J.T.Y. / Ma, Q. / Koh, S.H. / Mu, Y. / Miao, Y. / Gao, Y.G.
History
DepositionNov 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 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: PRF3


Theoretical massNumber of molelcules
Total (without water)14,0461
Polymers14,0461
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6310 Å2
Unit cell
Length a, b, c (Å)80.987, 52.862, 32.410
Angle α, β, γ (deg.)90.00, 110.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PRF3 / Profilin 3


Mass: 14045.962 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FE63
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 0.1M sodium acetate (pH 5.0), 1.42M ammonium sulfate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.457→43.4 Å / Num. obs: 44096 / % possible obs: 99 % / Redundancy: 3.26 % / CC1/2: 0.996 / Net I/σ(I): 8.77
Reflection shellResolution: 1.457→1.509 Å / Num. unique obs: 6286 / CC1/2: 0.634

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NUL

3nul


Resolution: 1.457→43.381 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 2079 4.76 %
Rwork0.1921 --
obs0.193 43672 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.457→43.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 0 49 1024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006994
X-RAY DIFFRACTIONf_angle_d0.8351350
X-RAY DIFFRACTIONf_dihedral_angle_d3.95360
X-RAY DIFFRACTIONf_chiral_restr0.079152
X-RAY DIFFRACTIONf_plane_restr0.006177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.457-1.49090.46281260.42712603X-RAY DIFFRACTION93
1.4909-1.52820.38651390.35962745X-RAY DIFFRACTION99
1.5282-1.56950.32751430.33622714X-RAY DIFFRACTION98
1.5695-1.61570.32541420.29112823X-RAY DIFFRACTION100
1.6157-1.66790.28741520.27082788X-RAY DIFFRACTION100
1.6679-1.72750.23731620.24592808X-RAY DIFFRACTION100
1.7275-1.79660.21461430.21652750X-RAY DIFFRACTION100
1.7966-1.87840.2391180.19462804X-RAY DIFFRACTION100
1.8784-1.97740.18591270.19812796X-RAY DIFFRACTION100
1.9774-2.10130.20521330.1922788X-RAY DIFFRACTION100
2.1013-2.26360.17241220.18982840X-RAY DIFFRACTION100
2.2636-2.49130.23611570.18792780X-RAY DIFFRACTION100
2.4913-2.85180.22861580.20152747X-RAY DIFFRACTION100
2.8518-3.59270.20161480.17992800X-RAY DIFFRACTION100
3.5927-43.40040.1741090.16332807X-RAY DIFFRACTION99

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