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- PDB-7w51: Crystal structure of fragmin domain-1 in complex with actin (ADP-form) -

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Basic information

Entry
Database: PDB / ID: 7w51
TitleCrystal structure of fragmin domain-1 in complex with actin (ADP-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 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 ...Striated Muscle Contraction / 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 / 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: 1.2 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)61,20511
Polymers60,3632
Non-polymers8429
Water15,853880
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-48 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.220, 91.141, 115.240
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 , 5 types, 889 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-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES-NaOH, pH 8.0, 16% 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: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.2→71.486 Å / Num. all: 182217 / Num. obs: 182217 / % possible obs: 97 % / Redundancy: 6.3 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Rsym value: 0.108 / Net I/av σ(I): 3.8 / Net I/σ(I): 8.1 / Num. measured all: 1142877
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.265.61.2560.6141418254640.5621.3791.2561.293.7
1.26-1.345.70.8430.9139428244650.3730.9240.843295.1
1.34-1.435.90.5791.3136297232420.2540.6330.5792.996
1.43-1.556.10.3512.2133812219540.1520.3830.3514.897.1
1.55-1.76.40.223.4130787203770.0930.2390.227.297.9
1.7-1.96.80.1524.6126553185950.0620.1640.15210.398.4
1.9-2.196.90.1135.8114432165850.0460.1220.11314.699.1
2.19-2.686.70.0867.194277141520.0360.0940.08617.799.5
2.68-3.797.40.077.681881111200.0280.0750.0722.399.9
3.79-37.08870.0688.14399262630.0270.0730.06823.498.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.6.02phasing
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W4Z

7w4z


Resolution: 1.2→30.31 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.176 9153 5.03 %
Rwork0.1506 172930 -
obs0.1519 182083 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.17 Å2 / Biso mean: 19.157 Å2 / Biso min: 7.87 Å2
Refinement stepCycle: final / Resolution: 1.2→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 50 943 5046
Biso mean--17.05 32.57 -
Num. residues----515
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 (%)
1.2-1.210.33112760.29875484576092
1.21-1.230.29763010.26745487578894
1.23-1.240.29492660.26225498576493
1.24-1.260.27543040.24995567587195
1.26-1.280.2882950.2495544583994
1.28-1.290.24523110.2425550586195
1.29-1.310.27132890.22695627591695
1.31-1.330.24522910.21925622591395
1.33-1.350.23743130.20345594590796
1.35-1.370.23333220.18745625594796
1.37-1.40.21042920.17565699599195
1.4-1.420.19573010.17145704600597
1.42-1.450.19142820.15945709599197
1.45-1.480.19293150.15095726604197
1.48-1.510.18453110.13845730604197
1.51-1.550.17753160.13025771608797
1.55-1.590.16552980.12455744604297
1.59-1.630.15513040.11365834613898
1.63-1.680.15083030.11555791609498
1.68-1.730.14962690.12115866613598
1.73-1.790.16462880.12645886617498
1.79-1.860.17173110.1345870618199
1.86-1.950.16593160.13975888620499
1.95-2.050.16953480.13665850619898
2.05-2.180.16793310.13385932626399
2.18-2.350.16413090.1425948625799
2.35-2.580.16122980.141760226320100
2.58-2.960.17213220.150560256347100
2.96-3.730.15853380.143760866424100
3.73-30.310.15543330.14746251658499

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