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- PDB-6iqj: crystal structure of Arabidopsis thaliana Profilin 2 complex with... -

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Basic information

Entry
Database: PDB / ID: 6iqj
Titlecrystal structure of Arabidopsis thaliana Profilin 2 complex with formin1
Components
  • Formin-like protein 1
  • Profilin-2
KeywordsPLANT PROTEIN / actin binding / regulate actin network
Function / homology
Function and homology information


inflorescence development / lateral root development / actin nucleation / leaf development / barbed-end actin filament capping / actin polymerization or depolymerization / chloroplast / defense response / actin filament binding / actin binding ...inflorescence development / lateral root development / actin nucleation / leaf development / barbed-end actin filament capping / actin polymerization or depolymerization / chloroplast / defense response / actin filament binding / actin binding / actin cytoskeleton organization / cytoskeleton / endoplasmic reticulum / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Formin-like family, plant / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Profilin conserved site / Profilin signature. / Profilin / Profilin ...Formin-like family, plant / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Profilin-2 / Formin-like protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.922 Å
AuthorsQiao, Z. / Gao, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Profilin 3 dynamictly regulate fomrin binding by its N terminal tail
Authors: Qiao, Z. / Gao, Y.
History
DepositionNov 8, 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

Downloads & links

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Assembly

Deposited unit
B: Profilin-2
A: Profilin-2
C: Formin-like protein 1
D: Formin-like protein 1


Theoretical massNumber of molelcules
Total (without water)30,7394
Polymers30,7394
Non-polymers00
Water4,288238
1
B: Profilin-2
D: Formin-like protein 1


Theoretical massNumber of molelcules
Total (without water)15,3692
Polymers15,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-9 kcal/mol
Surface area6600 Å2
MethodPISA
2
A: Profilin-2
C: Formin-like protein 1


Theoretical massNumber of molelcules
Total (without water)15,3692
Polymers15,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.523, 65.156, 73.533
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 Profilin-2 / PRF2


Mass: 14010.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PFN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42418
#2: Protein/peptide Formin-like protein 1 / AtFORMIN-8


Mass: 1358.646 Da / Num. of mol.: 2 / Fragment: UNP residues 524-536 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SE97
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 0.1M Bis-tris (pH 7.0), 2.0M ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.92→40.414 Å / Num. obs: 18928 / % possible obs: 97.37 % / Redundancy: 10 % / CC1/2: 0.998 / Net I/σ(I): 9.3
Reflection shellResolution: 1.923→1.991 Å / Num. unique obs: 759 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NUL

3nul


Resolution: 1.922→40.414 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 929 4.91 %
Rwork0.1834 --
obs0.1851 18916 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.922→40.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 238 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032173
X-RAY DIFFRACTIONf_angle_d0.5812956
X-RAY DIFFRACTIONf_dihedral_angle_d2.8551285
X-RAY DIFFRACTIONf_chiral_restr0.044315
X-RAY DIFFRACTIONf_plane_restr0.005393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9218-2.02310.31771050.22372252X-RAY DIFFRACTION87
2.0231-2.14990.21891420.20452502X-RAY DIFFRACTION97
2.1499-2.31590.21811240.18512582X-RAY DIFFRACTION99
2.3159-2.54890.23651410.19162611X-RAY DIFFRACTION100
2.5489-2.91760.24891190.18342645X-RAY DIFFRACTION100
2.9176-3.67550.18231410.16732633X-RAY DIFFRACTION98
3.6755-40.42310.20311570.17312762X-RAY DIFFRACTION100

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