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Yorodumi- PDB-3gaa: The crystal structure of the protein with unknown function from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gaa | ||||||
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Title | The crystal structure of the protein with unknown function from Thermoplasma acidophilum | ||||||
Components | uncharacterized protein Ta1441 | ||||||
Keywords | structural genomics / unknown function / The protein with unknown function from Thermoplasma acidophilum / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Zhang, R. / Borovilos, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the protein with unknown function from Thermoplasma acidophilum Authors: Zhang, R. / Borovilos, M. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gaa.cif.gz | 231.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gaa.ent.gz | 190 KB | Display | PDB format |
PDBx/mmJSON format | 3gaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gaa_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 3gaa_full_validation.pdf.gz | 525.4 KB | Display | |
Data in XML | 3gaa_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 3gaa_validation.cif.gz | 65.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/3gaa ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3gaa | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein existed as decamer. The second part of the decamer is generated by the axis: y,x,-z+1 |
-Components
#1: Protein | Mass: 27588.037 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: GI:10640783, Ta1441 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HIA0 #2: 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: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG4000,0.1M Mes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→101.02 Å / Num. all: 44574 / Num. obs: 44396 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.7→2.768 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.17 / Num. unique all: 3446 / % possible all: 97.53 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→101.02 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 28.768 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0 / ESU R: 0.618 / ESU R Free: 0.322 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 40.639 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→101.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.698→2.768 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 48.853 Å / Origin y: 87.215 Å / Origin z: 109.259 Å
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Refinement TLS group |
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