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- PDB-2vk3: Crystal structure of rat profilin 2a -

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Basic information

Entry
Database: PDB / ID: 2vk3
TitleCrystal structure of rat profilin 2a
ComponentsPROFILIN-2
KeywordsPROTEIN BINDING / PROFILIN / CYTOPLASM / ACETYLATION / CYTOSKELETON / ACTIN-BINDING / DISULFIDE BRIDGE / ALTERNATIVE SPLICING / PROTEIN-BINDING
Function / homology
Function and homology information


RHO GTPases Activate Formins / presynaptic actin cytoskeleton organization / negative regulation of ruffle assembly / modification of postsynaptic actin cytoskeleton / negative regulation of epithelial cell migration / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / regulation of synaptic vesicle exocytosis / positive regulation of actin filament polymerization ...RHO GTPases Activate Formins / presynaptic actin cytoskeleton organization / negative regulation of ruffle assembly / modification of postsynaptic actin cytoskeleton / negative regulation of epithelial cell migration / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / regulation of synaptic vesicle exocytosis / positive regulation of actin filament polymerization / actin monomer binding / positive regulation of stress fiber assembly / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / positive regulation of peptidyl-serine phosphorylation / presynapse / actin binding / postsynapse / cytoskeleton / protein stabilization / glutamatergic synapse / ATP hydrolysis activity / cytoplasm
Similarity search - Function
Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase ...Profilin1/2/3, vertebrate / 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
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Profilin-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHaikarainen, T. / Kursula, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure, Modifications and Ligand-Binding Properties of Rat Profilin 2A.
Authors: Haikarainen, T. / Chen, W.Q. / Lubec, G. / Kursula, P.
History
DepositionDec 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7516
Polymers15,1621
Non-polymers5895
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.100, 51.100, 67.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PROFILIN-2 / PROFILIN IIA / PROFILIN 2A


Mass: 15162.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BRIDGE BETWEEN CYS15 AND CYS16 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-4T-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9EPC6
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 4.5 / Details: 2M AMMONIUM SULPHATE, 1M NACL, PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9079
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9079 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 18939 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8F

2v8f


Resolution: 1.7→17.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.537 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 946 5 %RANDOM
Rwork0.173 ---
obs0.175 17987 99 %-
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: 17.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→17.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 33 220 1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221146
X-RAY DIFFRACTIONr_bond_other_d0.0020.02781
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9761538
X-RAY DIFFRACTIONr_angle_other_deg1.0953.0021896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6875149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11223.86444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3515188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.378156
X-RAY DIFFRACTIONr_chiral_restr0.1240.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021288
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02236
X-RAY DIFFRACTIONr_nbd_refined0.2240.2236
X-RAY DIFFRACTIONr_nbd_other0.2220.2901
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2576
X-RAY DIFFRACTIONr_nbtor_other0.0890.2633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4872897
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.21741138
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8846504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7338400
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 68
Rwork0.251 1288

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