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Yorodumi- PDB-4zj9: Small heat shock protein AgsA from Salmonella typhimurium: Alpha ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zj9 | ||||||
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Title | Small heat shock protein AgsA from Salmonella typhimurium: Alpha crystallin domain | ||||||
Components | Aggregation suppressing protein | ||||||
Keywords | CHAPERONE / small heat shock protein / crystallin / dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mani, N. / Suguna, K. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Multiple oligomeric structures of a bacterial small heat shock protein Authors: Mani, N. / Bhandari, S. / Moreno, R. / Hu, L. / Prasad, B.V. / Suguna, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zj9.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zj9.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zj9 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zj9 | HTTPS FTP |
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-Related structure data
Related structure data | 4zjaC 4zjdC 3w1zS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17103.096 Da / Num. of mol.: 1 / Fragment: UNP residues 12-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: agsA / Plasmid: pRSET C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D1MC98, UniProt: Q8ZPY6*PLUS |
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#2: Chemical | ChemComp-MPD / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.04 % / Description: Tetragonal crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% Pentaerythritol propoxylate (5/4 PO/OH), 0.1M MES-NaOH, 20% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.12 Å / Num. obs: 8413 / % possible obs: 99.8 % / Redundancy: 13.8 % / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W1Z Resolution: 2→34.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.865 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.159 / 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: 56.336 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.12 Å
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Refine LS restraints |
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