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- PDB-7rtx: Actophorin grown in microgravity -

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Basic information

Entry
Database: PDB / ID: 7rtx
TitleActophorin grown in microgravity
ComponentsActophorin
KeywordsMOTOR PROTEIN / microgravity
Function / homology
Function and homology information


actin filament depolymerization / actin filament binding / actin cytoskeleton / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLieberman, R.L. / Quirk, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Improved resolution crystal structure of Acanthamoeba actophorin reveals structural plasticity not induced by microgravity.
Authors: Quirk, S. / Lieberman, R.L.
History
DepositionAug 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Actophorin


Theoretical massNumber of molelcules
Total (without water)15,4441
Polymers15,4441
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.810, 45.800, 69.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Actophorin


Mass: 15444.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P37167
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.9 %
Description: Long (1 - 2 mm) rectangular cuboids with the other dimensions on the order of 0.05 - 0.1 mm. Crystals grow at room temperature in 3-5 days.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 mg/mL protein, 0.1 M MOPS, 16% Polyethylene glycol (8,000)
Temp details: 295 - 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→34.66 Å / Num. obs: 28851 / % possible obs: 99.49 % / Redundancy: 6.1 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07705 / Net I/σ(I): 11.63
Reflection shellResolution: 1.65→1.709 Å / Rmerge(I) obs: 0.8745 / Num. unique obs: 1542 / CC1/2: 0.816

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AHQ

1ahq


Resolution: 1.65→34.66 Å / SU ML: 0.2181 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 1813 6.28 %
Rwork0.188 27038 -
obs0.1902 28851 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.09 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 0 108 1162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211181
X-RAY DIFFRACTIONf_angle_d1.20151613
X-RAY DIFFRACTIONf_chiral_restr0.0828173
X-RAY DIFFRACTIONf_plane_restr0.0103220
X-RAY DIFFRACTIONf_dihedral_angle_d5.7436168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.37481390.33372121X-RAY DIFFRACTION99.56
1.69-1.740.30031460.27212109X-RAY DIFFRACTION99.87
1.74-1.80.29271420.24742105X-RAY DIFFRACTION99.78
1.8-1.870.25991400.2372107X-RAY DIFFRACTION99.29
1.87-1.940.28561430.21922091X-RAY DIFFRACTION98.76
1.94-2.030.28141390.22392113X-RAY DIFFRACTION99.03
2.03-2.130.23531390.20522074X-RAY DIFFRACTION97.75
2.14-2.270.26591300.19592021X-RAY DIFFRACTION95.26
2.27-2.440.211340.19212059X-RAY DIFFRACTION95.89
2.44-2.690.24611380.19892061X-RAY DIFFRACTION97.6
2.69-3.080.22911400.18512080X-RAY DIFFRACTION97.63
3.08-3.880.2011360.17382029X-RAY DIFFRACTION95.84
3.88-34.660.1821470.15312068X-RAY DIFFRACTION97.66
Refinement TLS params.Method: refined / Origin x: -16.5995468693 Å / Origin y: -3.75962173343 Å / Origin z: 6.66320871658 Å
111213212223313233
T0.192253756523 Å2-0.0197741896044 Å20.0488613032694 Å2-0.17835042038 Å2-0.0178737883493 Å2--0.194075317424 Å2
L2.33239306194 °20.328343764902 °20.55202306089 °2-2.39724982192 °20.573772125872 °2--2.38911333542 °2
S0.129695356045 Å °-0.0928096030339 Å °0.170802646495 Å °0.0981841866569 Å °-0.0609745294551 Å °-0.00500495192901 Å °-0.107319282486 Å °-0.125265334761 Å °-0.069110503162 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 134)

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