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- PDB-7aw8: Alpha-actinin in Rhodamnia argentea -

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Basic information

Entry
Database: PDB / ID: 7aw8
TitleAlpha-actinin in Rhodamnia argentea
ComponentsAlpha actinin, actin binding domain
KeywordsCELL CYCLE / Alpha actinin / actin binding
Function / homologyACETIC ACID / FORMIC ACID
Function and homology information
Biological speciesRhodamnia argentea (silver malletwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsPersson, K. / Backman, L.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other privateCarl Tyrggers foundation Sweden
CitationJournal: Febs Open Bio / Year: 2021
Title: Structural and functional characterization of a plant alpha-actinin.
Authors: Persson, K. / Backman, L.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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: Alpha actinin, actin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1868
Polymers31,8361
Non-polymers3507
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, This is a single actin binding domain of a larger protein (alpha-actinin)
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint2 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.219, 37.219, 290.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Alpha actinin, actin binding domain


Mass: 31835.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodamnia argentea (silver malletwood) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.93 Å3/Da / Density % sol: 32.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 3.1 M NaFormate 0.1 M NaAcetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.5→48.38 Å / Num. obs: 71951 / % possible obs: 99.9 % / Redundancy: 18.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.023 / Rrim(I) all: 0.098 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5316.40.8833048218550.9070.2220.9112.999.4
8.22-48.3814.20.04647333340.9990.0120.04837.299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.09 Å48.38 Å
Translation5.09 Å48.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A36

5a36


Resolution: 1.5→48.38 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1901 3578 4.97 %
Rwork0.1671 68373 -
obs0.1682 71951 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.34 Å2 / Biso mean: 32.8964 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 1.5→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 39 168 2158
Biso mean--43.5 36.7 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.30951300.25892523265399
1.52-1.540.25161480.257527282876100
1.54-1.560.26421370.247226102747100
1.56-1.590.2781320.236525592691100
1.59-1.610.29291440.242127432887100
1.61-1.640.25041320.224526082740100
1.64-1.670.25551370.218125882725100
1.67-1.70.24711480.207827362884100
1.7-1.730.2191370.202525352672100
1.73-1.760.23491360.196326852821100
1.76-1.80.22281300.195325482678100
1.8-1.840.21351410.193326962837100
1.84-1.890.22811350.1842617275299
1.89-1.940.20331390.181526302769100
1.94-20.20241350.174125742709100
2-2.060.23471380.17227312869100
2.06-2.140.17771370.169225892726100
2.14-2.220.21111390.156626392778100
2.22-2.320.17011420.159726802822100
2.32-2.450.21921340.157625662700100
2.45-2.60.19571330.161726332766100
2.6-2.80.16241410.161726492790100
2.8-3.080.18031380.160526402778100
3.08-3.520.16911280.155126052733100
3.53-4.440.15761460.127726172763100
4.44-48.380.17011410.17126442785100

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