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Yorodumi- PDB-4f0w: Crystal structure of type effector Tse1 C30A mutant from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f0w | ||||||
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Title | Crystal structure of type effector Tse1 C30A mutant from Pseudomonas aeruginousa | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | HYDROLASE / NlpC/P60 domain | ||||||
Function / homology | Function and homology information gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Zhang, H. / Gao, Z.Q. / Dong, Y.H. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa. Authors: Zhang, H. / Gao, Z.Q. / Su, X.D. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f0w.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f0w.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 4f0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f0w_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 4f0w_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 4f0w_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4f0w_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/4f0w ftp://data.pdbj.org/pub/pdb/validation_reports/f0/4f0w | HTTPS FTP |
-Related 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: 20164.676 Da / Num. of mol.: 1 / Mutation: C30A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2Q1 |
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#2: Chemical | ChemComp-MLI / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Sodium malonate pH 7.0, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2012 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→50 Å / Num. all: 48208 / Num. obs: 48208 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.47 / Num. unique all: 2300 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native paTse1 structure Resolution: 1.24→29.887 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 16.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.804 Å2 / ksol: 0.386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.24→29.887 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Origin x: 0.2085 Å / Origin y: 18.7054 Å / Origin z: 13.3183 Å
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Refinement TLS group | Selection details: ALL |