+Open data
-Basic information
Entry | Database: PDB / ID: 5zzb | ||||||
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Title | LokiProfilin2/Rabbit Actin Complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Actin / Archaea / Loki | ||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / actin binding / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lokiarchaeum sp. GC14_75 (archaea) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Robinson, R.C. / Akil, C. | ||||||
Citation | Journal: Nature / Year: 2018 Title: Genomes of Asgard archaea encode profilins that regulate actin. Authors: Akil, C. / Robinson, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zzb.cif.gz | 416.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zzb.ent.gz | 337.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/5zzb ftp://data.pdbj.org/pub/pdb/validation_reports/zz/5zzb | HTTPS FTP |
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-Related structure data
Related structure data | 5yedC 5yeeSC 5zzaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules BDAC
#1: Protein | Mass: 41374.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | Mass: 14788.970 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lokiarchaeum sp. GC14_75 (archaea) / Gene: Lokiarch_27400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F8XMN8 |
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-Non-polymers , 4 types, 484 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM PCTP 25% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.7 Å / Num. obs: 50253 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.961 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.073 / Rrim(I) all: 0.139 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2600 / CC1/2: 0.899 / Rpim(I) all: 0.185 / Rrim(I) all: 0.346 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YEE Resolution: 2.3→61.65 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.866 / SU B: 16.974 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.106 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→61.65 Å
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Refine LS restraints |
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