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- PDB-6ljc: Crystal structure of fragmin F2-F3 domains (calcium and magnesium... -

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Basic information

Entry
Database: PDB / ID: 6ljc
TitleCrystal structure of fragmin F2-F3 domains (calcium and magnesium condition)
ComponentsActin-binding protein fragmin P
KeywordsCYTOSOLIC PROTEIN / fragmin / gelsolin family protein / calcium regulation / actin filament severing
Function / homology
Function and homology information


actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / phosphatidylinositol-4,5-bisphosphate binding / actin filament binding / actin cytoskeleton / metal ion binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Actin-binding protein fragmin P
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTakeda, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K17708 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K07373 Japan
CitationJournal: J.Muscle Res.Cell.Motil. / Year: 2020
Title: Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin.
Authors: Takeda, S. / Fujiwara, I. / Sugimoto, Y. / Oda, T. / Narita, A. / Maeda, Y.
History
DepositionDec 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7169
Polymers23,1001
Non-polymers6158
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.590, 115.590, 42.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Actin-binding protein fragmin P


Mass: 23100.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

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Non-polymers , 7 types, 320 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG3350, ammonium sulphate, calcium chloride, magnesium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.85→42.22 Å / Num. obs: 27718 / % possible obs: 100 % / Redundancy: 8.571 % / Biso Wilson estimate: 37.138 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.073 / Χ2: 1.001 / Net I/σ(I): 22.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.968.4571.0941.9744500.7411.165100
1.96-2.18.6030.5753.9541710.9080.612100
2.1-2.278.6380.337.3838880.9670.351100
2.27-2.488.6350.19312.4935920.9880.206100
2.48-2.778.6360.11120.3632420.9960.118100
2.77-3.28.6280.06331.0528990.9990.067100
3.2-3.918.450.03555.3224390.9990.037100
3.91-5.518.6060.02474.29192810.025100
5.51-42.228.3240.0279.89110910.02199.2

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Processing

Software
NameVersionClassification
PHENIX1.15-3459refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ffk

3ffk


Resolution: 1.85→34.09 Å / SU ML: 0.2106 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.501
RfactorNum. reflection% reflection
Rfree0.2025 1385 5 %
Rwork0.1825 --
obs0.1835 27713 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 33 312 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331686
X-RAY DIFFRACTIONf_angle_d0.57542270
X-RAY DIFFRACTIONf_chiral_restr0.0433249
X-RAY DIFFRACTIONf_plane_restr0.0033292
X-RAY DIFFRACTIONf_dihedral_angle_d23.9073631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.30571380.31642622X-RAY DIFFRACTION99.93
1.92-20.27761370.24072614X-RAY DIFFRACTION100
2-2.090.26711370.23142602X-RAY DIFFRACTION100
2.09-2.20.24541380.20942615X-RAY DIFFRACTION100
2.2-2.330.21431370.20622616X-RAY DIFFRACTION100
2.33-2.510.24861390.20492632X-RAY DIFFRACTION100
2.51-2.770.231370.19532608X-RAY DIFFRACTION100
2.77-3.170.23611390.19092632X-RAY DIFFRACTION100
3.17-3.990.17161400.1582663X-RAY DIFFRACTION100
3.99-34.090.15311430.15032724X-RAY DIFFRACTION99.72

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