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Yorodumi- PDB-3erm: The crystal structure of a conserved protein with unknown functio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3erm | ||||||
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Title | The crystal structure of a conserved protein with unknown function from Pseudomonas syringae pv. tomato str. DC3000 | ||||||
Components | uncharacterized conserved protein | ||||||
Keywords | structural genomics / unknown function / APC85034 / PPSPTO1197 / seudomonas syringae pv. tomato str. DC3000 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | PSPTO_1197 like / Uncharacterised protein family YebG / YebG-like superfamily / YebG protein / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å | ||||||
Authors | Tan, K. / Zhou, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a conserved protein with unknown function from Pseudomonas syringae pv. tomato str. DC3000 Authors: Tan, K. / Zhou, 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 | 3erm.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3erm.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 3erm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3erm_validation.pdf.gz | 475.7 KB | Display | wwPDB validaton report |
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Full document | 3erm_full_validation.pdf.gz | 486.1 KB | Display | |
Data in XML | 3erm_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3erm_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3erm ftp://data.pdbj.org/pub/pdb/validation_reports/er/3erm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Details | Experimentally unknown. It is predicted that the chains A and B forms a dimer. The chains C and D forms dimers with their symmetry-related molecules by the same operator x+1, x-y+1, -z+1/6, respectively. The chain E forms a dimer with its symmetry related molecule by an operator x-y+1, -y, -z. |
-Components
#1: Protein | Mass: 10108.802 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: str. DC3000 Gene: Pseudomonas syringae pv. tomato, PSPTO1197, PSPTO_1197 Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q887T9 #2: Chemical | ChemComp-SO4 / | #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 grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M Bicine, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937, 0.97948 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.45→42 Å / Num. all: 13874 / Num. obs: 13874 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 43.6 | |||||||||
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.96 / Num. unique all: 666 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.45→41.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 25.429 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.462 / ESU R Free: 0.291 / 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: 45.064 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→41.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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