+Open data
-Basic information
Entry | Database: PDB / ID: 4eq8 | ||||||
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Title | Crystal structure of PA1844 from Pseudomonas aeruginosa PAO1 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Effector PROTEIN / TYPE VI SECRETION / T6S / TOXIN | ||||||
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 / SAD / Resolution: 1.392 Å | ||||||
Authors | Shang, G. / Li, N. / Zhang, J. / Lu, D. / Yu, Q. / Zhao, Y. / Liu, X. / Xu, S. / Gu, L. | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function. Authors: Shang, G. / Liu, X. / Lu, D. / Zhang, J. / Li, N. / Zhu, C. / Liu, S. / Yu, Q. / Zhao, Y. / Zhang, H. / Hu, J. / Cang, H. / Xu, S. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eq8.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eq8.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 4eq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4eq8_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 4eq8_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 4eq8_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 4eq8_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/4eq8 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/4eq8 | 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: 17717.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1 | ||
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#2: Chemical | #3: 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: 2.05 Å3/Da / Density % sol: 39.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 3350, 0.1 Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→50 Å / Num. all: 29529 / Num. obs: 29529 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.39→1.44 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2801 / Rsym value: 0.584 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.392→31.72 Å / SU ML: 0.13 / σ(F): 0.18 / σ(I): 0 / Phase error: 14.39 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.037 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.392→31.72 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: 14
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Refinement TLS params. | Method: refined / Origin x: 24.2092 Å / Origin y: 30.4898 Å / Origin z: 31.4178 Å
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Refinement TLS group | Selection details: ALL |