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- PDB-3dav: Schizosaccharomyces Pombe Profilin crystallized from Sodium formate -

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Basic information

Entry
Database: PDB / ID: 3dav
TitleSchizosaccharomyces Pombe Profilin crystallized from Sodium formate
ComponentsProfilin
KeywordsPROTEIN BINDING / profilin / yeast / pombe / protein-protein interaction / Actin-binding / Cytoplasm / Cytoskeleton
Function / homology
Function and homology information


cytogamy / actin cortical patch organization / cell cortex of cell tip / medial cortex / mitotic actomyosin contractile ring assembly / actin cortical patch / sequestering of actin monomers / mating projection tip / actin monomer binding / actin filament polymerization ...cytogamy / actin cortical patch organization / cell cortex of cell tip / medial cortex / mitotic actomyosin contractile ring assembly / actin cortical patch / sequestering of actin monomers / mating projection tip / actin monomer binding / actin filament polymerization / guanyl-nucleotide exchange factor activity / cell cortex
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 speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEzezika, O.C. / Nolen, B.J. / Pollard, T.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Incompatibility with Formin Cdc12p Prevents Human Profilin from Substituting for Fission Yeast Profilin: INSIGHTS FROM CRYSTAL STRUCTURES OF FISSION YEAST PROFILIN.
Authors: Ezezika, O.C. / Younger, N.S. / Lu, J. / Kaiser, D.A. / Corbin, Z.A. / Nolen, B.J. / Kovar, D.R. / Pollard, T.D.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Profilin
B: Profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,05211
Polymers26,8452
Non-polymers2079
Water4,161231
1
A: Profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4914
Polymers13,4221
Non-polymers693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5607
Polymers13,4221
Non-polymers1386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.873, 82.426, 39.742
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Profilin /


Mass: 13422.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: Schizosaccharomyces pombe / Gene: cdc3, SPAC4A8.15c / Plasmid: pMW-SpPRF / Production host: Escherichia coli (E. coli) / Strain (production host): B21(DE3) / References: UniProt: P39825
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 4.0 M sodium formate , VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11429 / % possible obs: 95.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Rsym value: 0.069 / Net I/σ(I): 15.28
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.03 / Num. unique all: 747 / Rsym value: 0.343 / % possible all: 64

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOLREPphasing
RefinementStarting model: 3D9Y

3d9y


Resolution: 2.2→41.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.947 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26 534 4.7 %RANDOM
Rwork0.174 ---
all0.176 10814 --
obs0.176 11348 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.058 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.11 Å2
2---0.45 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 9 231 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221904
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9682586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3175250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43324.11868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33915304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.637158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021414
X-RAY DIFFRACTIONr_nbd_refined0.1940.2965
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4670.21
X-RAY DIFFRACTIONr_mcbond_it0.2991.51238
X-RAY DIFFRACTIONr_mcangle_it0.56121972
X-RAY DIFFRACTIONr_scbond_it0.9033698
X-RAY DIFFRACTIONr_scangle_it1.54.5614
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 26 -
Rwork0.233 579 -
all-605 -
obs-579 69.94 %

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