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- PDB-7w50: Crystal structure of fragmin domain-1 in complex with actin (ADP-... -

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Basic information

Entry
Database: PDB / ID: 7w50
TitleCrystal structure of fragmin domain-1 in complex with actin (ADP-Pi-form)
Components
  • Actin, alpha skeletal muscle
  • Actin-binding protein fragmin P
KeywordsCONTRACTILE PROTEIN / actin dynamics / fragmin / gelsolin / ATP hydrolysis
Function / homology
Function and homology information


Striated Muscle Contraction / actin filament capping / actin polymerization or depolymerization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding ...Striated Muscle Contraction / actin filament capping / actin polymerization or depolymerization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Actin, alpha skeletal muscle / Actin-binding protein fragmin P
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsTakeda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K17708 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures and mechanisms of actin ATP hydrolysis.
Authors: Kanematsu, Y. / Narita, A. / Oda, T. / Koike, R. / Ota, M. / Takano, Y. / Moritsugu, K. / Fujiwara, I. / Tanaka, K. / Komatsu, H. / Nagae, T. / Watanabe, N. / Iwasa, M. / Maeda, Y. / Takeda, S.
History
DepositionNov 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,36612
Polymers60,3632
Non-polymers1,00310
Water15,763875
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-71 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.210, 91.060, 115.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#2: Protein Actin-binding protein fragmin P


Mass: 18253.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the first two residues (GP) were derived from expression tag
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

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Non-polymers , 6 types, 885 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na2HPO4, 18% PEG3350

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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: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.15→48.62 Å / Num. obs: 208131 / % possible obs: 97.8 % / Redundancy: 7.284 % / Biso Wilson estimate: 16.058 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Χ2: 0.948 / Net I/σ(I): 13.15
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
1.15-1.184.5470.8931.636605715581145280.5721.0193.2
1.18-1.215.5550.8022.18102615238145850.6780.88595.7
1.21-1.257.0930.7552.6310112814818142570.7810.81496.2
1.25-1.297.1090.6443.099854814316138620.8320.69496.8
1.29-1.337.1290.5343.679670813987135660.8810.57597
1.33-1.377.1390.4524.349377913468131370.9080.48797.5
1.37-1.437.1580.3695.299127813060127520.9390.39797.6
1.43-1.487.170.2856.78838612532123270.9630.30798.4
1.48-1.557.1910.2168.738519712067118480.9780.23398.2
1.55-1.637.1920.16910.878210111542114150.9870.18298.9
1.63-1.717.1970.13812.987825510973108740.9910.14899.1
1.71-1.827.1970.10815.887435710416103310.9940.11799.2
1.82-1.947.1720.08418.8269782978097300.9960.09199.5
1.94-2.17.0880.06823.4664655915891220.9970.07399.6
2.1-2.37.0560.05728.9859327844484080.9980.06199.6
2.3-2.577.2820.0532.5455618765276380.9980.05499.8
2.57-2.9711.7030.05639.7479334678467790.9990.05999.9
2.97-3.6412.0290.04547.2769614579057870.9990.04799.9
3.64-5.1411.6240.0454.0252763453945390.9990.042100
5.14-48.6210.6950.03951.5127990262226170.9990.04199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
MOLREP11.5.02phasing
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W4Z

7w4z


Resolution: 1.15→48.62 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1617 10405 5 %
Rwork0.1418 197726 -
obs0.1428 208131 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.65 Å2 / Biso mean: 17.8691 Å2 / Biso min: 5.39 Å2
Refinement stepCycle: final / Resolution: 1.15→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 62 922 5048
Biso mean--18.56 30.53 -
Num. residues----518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.160.29153210.28776096641791
1.16-1.180.25813330.24376328666195
1.18-1.190.26043350.22666365670095
1.19-1.210.23233350.2116362669796
1.21-1.220.21293410.19486477681896
1.22-1.240.2273370.1926418675596
1.24-1.260.21953380.18596422676096
1.26-1.280.20863410.17596475681697
1.28-1.30.19153420.16956488683097
1.3-1.320.19263410.16076478681997
1.32-1.340.18043420.15226500684297
1.34-1.360.17083430.14676521686497
1.36-1.390.19543430.14456517686098
1.39-1.420.19073470.13836592693998
1.42-1.450.15723450.12896556690198
1.45-1.480.15413460.12246579692598
1.48-1.520.14183480.11746616696498
1.52-1.560.14333490.10996625697499
1.56-1.610.13693490.10886650699999
1.61-1.660.13173490.11066638698799
1.66-1.720.15073520.11686683703599
1.72-1.790.14883520.1216680703299
1.79-1.870.14853520.130966887040100
1.87-1.970.15083550.13267467101100
1.97-2.090.14563550.129667487103100
2.09-2.250.15593570.1367877144100
2.25-2.480.15813580.139668007158100
2.48-2.840.17433600.149168357195100
2.84-3.570.16253650.145169317296100
3.57-48.620.1393740.139671257499100

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