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Yorodumi- PDB-3gtz: Crystal structure of a putative translation initiation inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gtz | ||||||
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Title | Crystal structure of a putative translation initiation inhibitor from Salmonella typhimurium | ||||||
Components | Putative translation initiation inhibitor | ||||||
Keywords | structural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information RutC family, YoaB-like / RidA, conserved site / Uncharacterized protein family UPF0076 signature. / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Bonanno, J.B. / Freeman, J. / Bain, K.T. / Miller, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative translation initiation inhibitor from Salmonella typhimurium Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Miller, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gtz.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gtz.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gtz_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 3gtz_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 3gtz_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3gtz_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/3gtz ftp://data.pdbj.org/pub/pdb/validation_reports/gt/3gtz | 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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-Components
#1: Protein | Mass: 13814.569 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: STM1822, yoaB / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZP08 #2: Chemical | ChemComp-GOL / | #3: 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: 4.01 Å3/Da / Density % sol: 69.33 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 10% PEG 6K, 2.0M sodium chloride, pH 7.0, vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 26, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→22.875 Å / Num. all: 24036 / Num. obs: 24012 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.7 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 33.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 29.1 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 8.7 / Num. measured all: 100080 / Num. unique all: 3436 / Rsym value: 0.436 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.235 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.723 / SU B: 7.963 / SU ML: 0.185 / SU R Cruickshank DPI: 0.279 / SU Rfree: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.279 / ESU R Free: 0.228 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.76 Å2 / Biso mean: 52.883 Å2 / Biso min: 22.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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