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- PDB-3nul: Profilin I from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 3nul
TitleProfilin I from Arabidopsis thaliana
ComponentsPROFILIN I
KeywordsACTIN BINDING PROTEIN / PROFILIN / CYTOSKELETON
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 / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsThorn, K. / Christensen, H.E.M. / Shigeta, R. / Huddler, D. / Chua, N.-H. / Shalaby, L. / 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
DepositionNov 27, 1996Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROFILIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5694
Polymers14,2891
Non-polymers2803
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.040, 43.070, 59.450
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 I


Mass: 14288.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cellular location: CELLULAR CYTOSKELETON / Production host: Escherichia coli (E. coli) / References: UniProt: Q42449
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34.69 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95, 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 15, 1996 / Details: NI/RH MIRRORS
RadiationMonochromator: CRYSTALLINE MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
21.11
ReflectionResolution: 1.6→30 Å / Num. obs: 32355 / % possible obs: 96 % / Observed criterion σ(I): 5 / Redundancy: 4.5 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.055 / Net I/σ(I): 18.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.189 / % possible all: 78.8
Reflection
*PLUS
Num. measured all: 146788

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→8 Å / Data cutoff high absF: 4200000000 / Data cutoff low absF: 0 / Cross valid method: DURING REFINEMENT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.204 880 6 %RANDOM
Rwork0.1808 ---
obs0.1808 26492 96 %-
Displacement parametersBiso mean: 11.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.18 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 17 99 1111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.878
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.11
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.625
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: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2596 109 6.25 %
Rwork0.2562 1635 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROGOLPAR.PRO
X-RAY DIFFRACTION2SOLVPAR.PROSEMETPAR.PRO
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2049
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.115
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.625

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