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- PDB-6ljd: Crystal structure of fragmin F2-F3 domains (calcium condition) -

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Basic information

Entry
Database: PDB / ID: 6ljd
TitleCrystal structure of fragmin F2-F3 domains (calcium 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 / actin polymerization or depolymerization / barbed-end actin filament capping / 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 / molecular replacement / Resolution: 2.15 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)23,6398
Polymers23,1001
Non-polymers5397
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.830, 115.830, 42.110
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 , 6 types, 174 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, ammonium sulphate, calcium 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: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.15→42.113 Å / Num. obs: 17807 / % possible obs: 100 % / Redundancy: 8.553 % / Biso Wilson estimate: 46.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.103 / Χ2: 1.004 / Net I/σ(I): 16.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.288.5021.0452.0428620.751.113100
2.28-2.448.6360.7273.126550.8620.774100
2.44-2.638.6360.4265.2725050.9450.453100
2.63-2.888.650.2478.8922930.9840.263100
2.88-3.228.610.13415.1821000.9950.143100
3.22-3.728.5680.07127.5418470.9980.076100
3.72-4.548.3930.04740.9615750.9990.05100
4.54-6.388.4710.03944.4512340.9990.041100
6.38-42.1138.1580.03150.797360.9990.03399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.15refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ffk

3ffk


Resolution: 2.15→38.83 Å / SU ML: 0.2196 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.6887
RfactorNum. reflection% reflection
Rfree0.2188 891 5 %
Rwork0.1927 --
obs0.194 17803 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 27 167 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471664
X-RAY DIFFRACTIONf_angle_d0.70362242
X-RAY DIFFRACTIONf_chiral_restr0.0443246
X-RAY DIFFRACTIONf_plane_restr0.004289
X-RAY DIFFRACTIONf_dihedral_angle_d23.138618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.290.27151480.25342799X-RAY DIFFRACTION99.93
2.29-2.460.26711480.24252812X-RAY DIFFRACTION100
2.46-2.710.26291460.21532774X-RAY DIFFRACTION100
2.71-3.10.26671470.21692804X-RAY DIFFRACTION100
3.1-3.910.18811490.18592817X-RAY DIFFRACTION100
3.91-38.830.19431530.16532906X-RAY DIFFRACTION99.93

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