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- PDB-7sog: Thermostable actophorin -

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Basic information

Entry
Database: PDB / ID: 7sog
TitleThermostable actophorin
ComponentsActophorin
KeywordsMOTOR PROTEIN / MUTAGENESIS
Function / homology
Function and homology information


actin filament depolymerization / actin cytoskeleton / actin binding / 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
NICKEL (II) ION / Actophorin
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLieberman, R.L. / Quirk, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structure and activity of a thermally stable mutant of Acanthamoeba actophorin.
Authors: Quirk, S. / Lieberman, R.L.
History
DepositionOct 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: 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
B: Actophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6016
Polymers30,3662
Non-polymers2354
Water3,333185
1
A: Actophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3013
Polymers15,1831
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Actophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3013
Polymers15,1831
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.720, 41.290, 55.500
Angle α, β, γ (deg.)90.000, 95.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Actophorin


Mass: 15183.150 Da / Num. of mol.: 2
Mutation: S2P, H21K, Q22K, T27I, M30L, A32D, S33D, H41K, K53L, S54A, R59N, Q71E, T81V, T99A, T101S, S104A, V110D, A122D, S130K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P37167
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, NISO4, MES pH6.5

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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: 1.74→36.58 Å / Num. obs: 24315 / % possible obs: 94.92 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05504 / Rrim(I) all: 0.0655 / Net I/σ(I): 13.1
Reflection shellResolution: 1.74→1.802 Å / Rmerge(I) obs: 0.6171 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 2410 / CC1/2: 0.769 / Rrim(I) all: 0.7272 / % possible all: 89.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RTX

7rtx


Resolution: 1.74→36.58 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 1979 8.3 %
Rwork0.1907 21867 -
obs0.1936 23846 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.12 Å2
Refinement stepCycle: LAST / Resolution: 1.74→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 4 185 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752209
X-RAY DIFFRACTIONf_angle_d0.74442994
X-RAY DIFFRACTIONf_chiral_restr0.0505323
X-RAY DIFFRACTIONf_plane_restr0.0056401
X-RAY DIFFRACTIONf_dihedral_angle_d7.7249302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.34221240.29821489X-RAY DIFFRACTION89.86
1.78-1.830.30131370.28631480X-RAY DIFFRACTION92.24
1.83-1.890.25391400.24641526X-RAY DIFFRACTION92.71
1.89-1.950.29161410.2231539X-RAY DIFFRACTION95.35
1.95-2.020.27541360.2141553X-RAY DIFFRACTION95.91
2.02-2.10.2381400.20611585X-RAY DIFFRACTION95.25
2.1-2.190.25111490.20241555X-RAY DIFFRACTION95.89
2.19-2.310.26211340.18691488X-RAY DIFFRACTION90.72
2.31-2.450.22181460.19261590X-RAY DIFFRACTION95.86
2.45-2.640.2211370.19671616X-RAY DIFFRACTION98.93
2.64-2.910.25791510.18991616X-RAY DIFFRACTION98.33
2.91-3.330.18931430.18271613X-RAY DIFFRACTION97.66
3.33-4.190.19151490.15911594X-RAY DIFFRACTION95.61
4.19-36.580.20181520.17821623X-RAY DIFFRACTION94.72

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