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- PDB-1ypr: SACCHAROMYCES CEREVISIAE (YEAST) PROFILIN -

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Basic information

Entry
Database: PDB / ID: 1ypr
TitleSACCHAROMYCES CEREVISIAE (YEAST) PROFILIN
ComponentsPROFILIN
KeywordsACTIN-BINDING PROTEIN / PROFILIN / CYTOSKELETON
Function / homology
Function and homology information


positive regulation of formin-nucleated actin cable assembly / mitotic actomyosin contractile ring assembly / proline-rich region binding / actin monomer binding / intracellular transport / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEads, J.C. / Mahoney, N.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 1998
Title: Structure determination and characterization of Saccharomyces cerevisiae profilin
Authors: Eads, J.C. / Mahoney, N.M. / Vorobiev, S. / Haarer, B.K. / Almo, S.C.
History
DepositionJun 26, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROFILIN
B: PROFILIN


Theoretical massNumber of molelcules
Total (without water)27,1182
Polymers27,1182
Non-polymers00
Water70339
1
A: PROFILIN


Theoretical massNumber of molelcules
Total (without water)13,5591
Polymers13,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROFILIN


Theoretical massNumber of molelcules
Total (without water)13,5591
Polymers13,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.100, 58.100, 151.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.427531, 0.806755, -0.407876), (-0.624338, 0.589808, 0.51218), (0.653773, 0.03568, 0.755849)
Vector: 16.9281, -18.738, -32.3712)

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Components

#1: Protein PROFILIN


Mass: 13559.190 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.72 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5 / Details: 1.0 M LI SULFATE, 0.1 M TRIS, PH 8.5, 0.01M NICL2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-8 mg/mlyeast profilin1drop
23.8-4.0 Msodium formate1reservoir
31.0 Mlithium sulfate1reservoir
40.1 MTris-HCl1reservoir
50.01 M1reservoirNiCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. obs: 12068 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.064 / Net I/σ(I): 10.75
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2.75 / Rsym value: 0.213 / % possible all: 77.5
Reflection
*PLUS
Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Lowest resolution: 2.4 Å / % possible obs: 77.5 % / Rmerge(I) obs: 0.213

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACANTHAMOEBA PROFILIN P1

Resolution: 2.3→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.22 620 5 %RANDOM
Rwork0.168 ---
obs0.168 11875 92.9 %-
Displacement parametersBiso mean: 34.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 0 39 1951
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_deg1.468
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
Refine LS restraints NCSNCS model details: RESTRAINTS, IN EARLY STAGES OF REFINEMENT
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.299 67 4.2 %
Rwork0.286 1100 -
obs--73 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor obs: 0.286

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