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- PDB-5ivu: Crystal Structure of Streptomyces griseoflavus Cofilin -

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Basic information

Entry
Database: PDB / ID: 5ivu
TitleCrystal Structure of Streptomyces griseoflavus Cofilin
ComponentsCofilin
KeywordsACTIN-BINDING PROTEIN / cytoskeleton / actin
Function / homology
Function and homology information


actin filament depolymerization / actin cytoskeleton / actin binding
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSchwebach, C. / Sotomayor, M. / Kudryashov, D.S.
CitationJournal: To Be Published
Title: Crystal Structure of Streptomyces griseoflavus Cofilin
Authors: Schwebach, C. / Kudryashov, D.S.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cofilin
B: Cofilin


Theoretical massNumber of molelcules
Total (without water)31,8682
Polymers31,8682
Non-polymers00
Water55831
1
A: Cofilin


Theoretical massNumber of molelcules
Total (without water)15,9341
Polymers15,9341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cofilin


Theoretical massNumber of molelcules
Total (without water)15,9341
Polymers15,9341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.927, 65.937, 70.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 6 - 138 / Label seq-ID: 6 - 138

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cofilin


Mass: 15933.913 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9XKI5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris HCl, 25% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.42→30 Å / Num. obs: 9995 / % possible obs: 96.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.86
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.98 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I2Q

2i2q


Resolution: 2.42→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.5 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.905 / ESU R Free: 0.331 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27908 503 5.2 %RANDOM
Rwork0.22529 ---
obs0.2281 9143 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.42→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 0 31 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192087
X-RAY DIFFRACTIONr_bond_other_d0.0040.021984
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9572811
X-RAY DIFFRACTIONr_angle_other_deg1.12934577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33725.347101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.88159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022338
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02457
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2594.7251027
X-RAY DIFFRACTIONr_mcbond_other2.2574.7231026
X-RAY DIFFRACTIONr_mcangle_it3.777.061275
X-RAY DIFFRACTIONr_mcangle_other3.7697.0631276
X-RAY DIFFRACTIONr_scbond_it2.354.9351060
X-RAY DIFFRACTIONr_scbond_other2.354.9351060
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9667.2451536
X-RAY DIFFRACTIONr_long_range_B_refined6.25535.3942234
X-RAY DIFFRACTIONr_long_range_B_other6.25335.4122235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14396 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.412→2.474 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 39 -
Rwork0.314 609 -
obs--91.27 %

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