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

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Basic information

Entry
Database: PDB / ID: 6iqk
Titlecrystal structure of Arabidopsis thaliana Profilin 3
Components
  • AtPRF3
  • Profilin-5
KeywordsPLANT PROTEIN / actin binding / regulate actin network
Function / homology
Function and homology information


sequestering of actin monomers / 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: 3.6 Å
AuthorsQiao, Z. / Gao, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) 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 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Profilin-5
B: Profilin-5
C: Profilin-5
D: Profilin-5
E: Profilin-5
F: Profilin-5
I: Profilin-5
J: Profilin-5
G: Profilin-5
H: Profilin-5
K: AtPRF3


Theoretical massNumber of molelcules
Total (without water)172,06611
Polymers172,06611
Non-polymers00
Water0
1
A: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
I: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
J: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
G: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
H: Profilin-5


Theoretical massNumber of molelcules
Total (without water)14,9581
Polymers14,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: AtPRF3


Theoretical massNumber of molelcules
Total (without water)22,4861
Polymers22,4861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.900, 153.370, 196.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Profilin-5 /


Mass: 14958.007 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRO5, PRF3, At5g56600, MIK19.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FE63
#2: Protein AtPRF3


Mass: 22485.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
Sequence detailsAuthors state that more than 10 copies present in the ASU because the resolution is low, only 3.6. ...Authors state that more than 10 copies present in the ASU because the resolution is low, only 3.6. The K chain consisted of unidentified residues which present in the Fo-Fc map. They were difficult to be modelled as target protein because of the low resolution. Therefore, the residue numbers are meaningless for the K chain.

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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: 6.52 Å3/Da / Density % sol: 81.14 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.1M Tris HCl (pH 7.8), 0.9M sodium citrate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→49.24 Å / Num. obs: 48279 / % possible obs: 99.8 % / Redundancy: 15 % / Biso Wilson estimate: 115.08 Å2 / CC1/2: 0.991 / Net I/σ(I): 6
Reflection shellResolution: 3.6→3.729 Å / Num. unique obs: 48279 / CC1/2: 0.275

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→49.24 Å / SU ML: 0.5867 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.0637
RfactorNum. reflection% reflection
Rfree0.3465 4822 10 %
Rwork0.309 --
obs0.3128 48230 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 123.99 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11558 0 0 0 11558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211720
X-RAY DIFFRACTIONf_angle_d0.549415916
X-RAY DIFFRACTIONf_chiral_restr0.04071866
X-RAY DIFFRACTIONf_plane_restr0.00352088
X-RAY DIFFRACTIONf_dihedral_angle_d2.28856948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.640.45651570.44991416X-RAY DIFFRACTION99.75
3.64-3.680.47621600.41141437X-RAY DIFFRACTION99.87
3.68-3.730.38921600.38711433X-RAY DIFFRACTION99.75
3.73-3.780.32471560.37091412X-RAY DIFFRACTION99.87
3.78-3.830.41861570.37811415X-RAY DIFFRACTION100
3.83-3.880.32441600.35211438X-RAY DIFFRACTION99.81
3.88-3.930.37231590.36871437X-RAY DIFFRACTION99.56
3.93-3.990.3521580.33071424X-RAY DIFFRACTION100
3.99-4.050.36171590.31891428X-RAY DIFFRACTION99.62
4.05-4.120.35031590.30421427X-RAY DIFFRACTION99.87
4.12-4.190.32681610.30451447X-RAY DIFFRACTION99.88
4.19-4.270.36971580.32411422X-RAY DIFFRACTION100
4.27-4.350.3591590.30921431X-RAY DIFFRACTION99.87
4.35-4.440.32811580.29971429X-RAY DIFFRACTION100
4.44-4.540.35561620.31111455X-RAY DIFFRACTION100
4.54-4.640.2751590.30031428X-RAY DIFFRACTION99.81
4.64-4.760.33521570.30021415X-RAY DIFFRACTION99.94
4.76-4.880.34071640.30151473X-RAY DIFFRACTION100
4.88-5.030.38661590.32391436X-RAY DIFFRACTION100
5.03-5.190.35111590.32261441X-RAY DIFFRACTION99.94
5.19-5.380.36091600.31061439X-RAY DIFFRACTION99.94
5.38-5.590.37641620.29741456X-RAY DIFFRACTION100
5.59-5.850.3361620.29861453X-RAY DIFFRACTION100
5.85-6.150.37971630.30741467X-RAY DIFFRACTION100
6.15-6.540.36891600.31091440X-RAY DIFFRACTION99.88
6.54-7.040.40071650.29141483X-RAY DIFFRACTION100
7.04-7.750.30651630.28451469X-RAY DIFFRACTION100
7.75-8.860.32261660.24671496X-RAY DIFFRACTION100
8.86-11.140.3071660.25491493X-RAY DIFFRACTION99.64
11.14-49.240.32111740.33171568X-RAY DIFFRACTION98.92
Refinement TLS params.Method: refined / Origin x: -32.0444146369 Å / Origin y: 41.7104655935 Å / Origin z: -44.2406648976 Å
111213212223313233
T0.698703648828 Å20.00896440696883 Å2-0.054764204691 Å2-0.688819741083 Å2-0.0635668074947 Å2--0.646033475811 Å2
L0.08933399709 °20.0924606651324 °2-0.0566836463306 °2-0.238612418982 °2-0.131179919336 °2--0.224348287097 °2
S-0.0318834879131 Å °0.0676675173102 Å °0.0374148229726 Å °-0.00722634833439 Å °0.0335590624313 Å °0.00730855320645 Å °-0.015311239481 Å °-0.0608524473367 Å °0.033984790287 Å °
Refinement TLS groupSelection details: all

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