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- PDB-1a0k: PROFILIN I FROM ARABIDOPSIS THALIANA -

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Basic information

Entry
Database: PDB / ID: 1a0k
TitlePROFILIN I FROM ARABIDOPSIS THALIANA
ComponentsPROFILIN
KeywordsCYTOSKELETON / PROFILIN / ACTIN-BINDING
Function / homology
Function and homology information


inflorescence development / unidimensional cell growth / lateral root development / phragmoplast / leaf development / plasmodesma / actin polymerization or depolymerization / defense response / spindle / actin binding ...inflorescence development / unidimensional cell growth / lateral root development / phragmoplast / leaf development / plasmodesma / actin polymerization or depolymerization / defense response / spindle / actin binding / nucleolus / mitochondrion / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShigeta Junior, R. / Huddler, D. / Lindberg, U. / Schutt, C.E.
Citation
Journal: Structure / Year: 1997
Title: The crystal structure of a major allergen from plants.
Authors: Thorn, K.S. / Christensen, H.E. / Shigeta, R. / Huddler, D. / Shalaby, L. / Lindberg, U. / Chua, N.H. / Schutt, C.E.
#1: Journal: Plant J. / Year: 1996
Title: Arabidopsis Profilins are Functionally Similar to Yeast Profilins: Identification of a Vascular Bundle-Specific Profilin and a Pollen-Specific Profilin
Authors: Christensen, H.E. / Ramachandran, S. / Tan, C.T. / Surana, U. / Dong, C.H. / Chua, N.H.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Structure Determination of Bovine Profilin at 2.0 A Resolution
Authors: Cedergren-Zeppezauer, E.S. / Goonesekere, N.C. / Rozycki, M.D. / Myslik, J.C. / Dauter, Z. / Lindberg, U. / Schutt, C.E.
#3: Journal: Nature / Year: 1993
Title: The Structure of Crystalline Profilin-Beta-Actin
Authors: Schutt, C.E. / Myslik, J.C. / Rozycki, M.D. / Goonesekere, N.C. / Lindberg, U.
History
DepositionDec 2, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROFILIN


Theoretical massNumber of molelcules
Total (without water)14,2791
Polymers14,2791
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.050, 43.530, 59.870
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


Mass: 14279.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: COLUMBIA / Cell line: BL21 / Cellular location: CELLULAR CYTOSKELETON / Gene: PFN / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q42449
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.9 Å3/Da / Density % sol: 22 %
Crystal growpH: 5
Details: 2.0 M AMMONIUM SULFATE, 0.1 M CITRATE PH 5.0, 10 MM DTT, 0.2 MM EDTA
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate1reservoir
20.1 Mcitrate1reservoir
310 mMDTT1reservoir
40.2 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 5530 / % possible obs: 90.4 % / Observed criterion σ(I): 5 / Redundancy: 2.6 % / Biso Wilson estimate: 4.02 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 0.2176
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.13 / Rsym value: 0.129 / % possible all: 55.5
Reflection
*PLUS
Num. measured all: 48373

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NUL

3nul


Resolution: 2.2→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Cross valid method: DURING REFINEMENT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.238 418 7 %RANDOM
Rwork0.172 ---
obs0.172 5530 91.23 %-
Displacement parametersBiso mean: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.02268 Å20.00818 Å2-0.01218 Å2
2---0.01178 Å20.00154 Å2
3---0.09292 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.12 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 26 1286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.907
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.65
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.568
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2483 33 7.84 %
Rwork0.2104 388 -
obs--61.15 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2SOLVPAR.PRO
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.568

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