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- PDB-6kwz: Crystal structure of fragmin F3 domain with calcium ion -

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Basic information

Entry
Database: PDB / ID: 6kwz
TitleCrystal structure of fragmin F3 domain with calcium ion
ComponentsActin-binding protein fragmin P
KeywordsCYTOSOLIC PROTEIN / fragmin / gelsolin family protein / calcium regulation / actin filament severing
Function / homology
Function and homology information


actin filament binding
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
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: 1.551 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
DepositionSep 9, 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
A: Actin-binding protein fragmin P
B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6454
Polymers21,5642
Non-polymers802
Water4,720262
1
A: Actin-binding protein fragmin P
hetero molecules

B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6454
Polymers21,5642
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_644-x+1,y-1/2,-z-1/21
Buried area1380 Å2
ΔGint-31 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.648, 55.076, 69.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Actin-binding protein fragmin P


Mass: 10782.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM MES-NaOH (pH 6.0), 20% PEG 3350

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.55→35.596 Å / Num. obs: 26672 / % possible obs: 99.8 % / Redundancy: 6.587 % / Biso Wilson estimate: 26.262 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 1 / Net I/σ(I): 15.02 / Num. measured all: 175682
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.656.0611.3121.5625407423141920.6761.43199.1
1.65-1.766.2780.8652.4625125400540020.8680.94199.9
1.76-1.96.4430.4814.4224154375037490.9580.522100
1.9-2.086.6380.2418.4522794343434340.9860.262100
2.08-2.336.8610.14313.821591314831470.9950.155100
2.33-2.687.0560.09620.0619616278127800.9970.104100
2.68-3.286.8640.05730.2116342238123810.9990.061100
3.28-4.637.0610.02953.4713275188218800.9990.03199.9
4.63-35.5966.6650.02360.47378111311070.9990.02599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.15_3459: ???refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFK

3ffk


Resolution: 1.551→35.596 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.07
RfactorNum. reflection% reflection
Rfree0.2164 1333 5 %
Rwork0.1907 --
obs0.192 26655 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.86 Å2 / Biso mean: 24.6037 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: final / Resolution: 1.551→35.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 2 268 1798
Biso mean--18.34 34.45 -
Num. residues----196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5513-1.60670.35671280.3617245199
1.6067-1.67110.36781320.30322509100
1.6711-1.74710.27941300.25912473100
1.7471-1.83920.30321330.22612514100
1.8392-1.95450.23411320.19712511100
1.9545-2.10530.1961330.17682513100
2.1053-2.31720.20491320.17572522100
2.3172-2.65240.21951350.18822549100
2.6524-3.34130.1941360.18472587100
3.3413-35.5960.18581420.16092693100

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