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- PDB-1k0k: Yeast Profilin, Cubic Crystal Form -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1k0k
TitleYeast Profilin, Cubic Crystal Form
ComponentsPROFILIN
KeywordsCONTRACTILE PROTEIN / ACTIN-BINDING PROTEIN / PIP2 BINDING PROTEIN / POLY-L-PROLINE BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of formin-nucleated actin cable assembly / mitotic actomyosin contractile ring assembly / sequestering of actin monomers / proline-rich region binding / actin monomer binding / intracellular transport / phosphatidylinositol-4,5-bisphosphate binding / cell cortex / cytoskeleton / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVorobiev, S. / Fedorov, A.A. / Almo, S.C.
Citation
Journal: To be Published
Title: A Comparative Structural Analysis of Profilins
Authors: Vorobiev, S. / Fedorov, A.A. / Almo, S.C.
#1: Journal: Biochemistry / Year: 1998
Title: Structure Determination and Characterization of Saccharomyces Cerevisae Profilin
Authors: Eads, J.C. / Mahoney, N.M. / Vorobiev, S. / Bresnick, A.R. / Wen, K.K. / Rubenstein, P.A. / Haarer, B.K. / Almo, S.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: X-Ray Structures of Isoforms of the Actin-Binding Protein Profilin That Differ in their Affinity for Phosphatidylinositol Phosphates
Authors: Fedorov, A.A. / Magnus, K.A. / Graupe, M.H. / Lattman, E.E. / Pollard, T.D. / Almo, S.C.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Purification, Characterization and Crystallization of Human Platelet Profilin Expressed in Escherichia Coli
Authors: Fedorov, A.A. / Pollard, T.D. / Almo, S.C.
#4: Journal: Structure / Year: 1997
Title: The Molecular Basis for Allergen Cross-Reactivity: Crystal Structure and Ige-Epitope Mapping of Birch Pollen Profilin
Authors: Fedorov, A.A. / Ball, T. / Mahoney, N.M. / Valenta, R. / Almo, S.C.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6512
Polymers13,5591
Non-polymers921
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.682, 126.682, 126.682
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number212
Space group name H-MP4332
DetailsThe biological assembly is a monomer

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Components

#1: Protein PROFILIN /


Mass: 13559.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P07274
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 6.165 Å3/Da / Density % sol: 79.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium format, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 14401 / Num. obs: 14401 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 45.3
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 12.9 / % possible all: 92

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YPR

1ypr


Resolution: 2.35→20 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1427 10.2 %RANDOM
Rwork0.211 ---
all0.222 14401 --
obs0.214 14013 93.5 %-
Solvent computationSolvent model: flat model / Bsol: 76.5199 Å2 / ksol: 0.391558 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 6 81 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it3.261.5
X-RAY DIFFRACTIONc_mcangle_it5.32
X-RAY DIFFRACTIONc_scbond_it5.092
X-RAY DIFFRACTIONc_scangle_it7.872.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 196 9.3 %
Rwork0.255 1901 -
obs-2097 86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gol_xplor_par.txtgol_xplor_top.txt

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