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Yorodumi- PDB-8cib: Structural and functional analysis of the Pseudomonas aeruginosa ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cib | |||||||||
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Title | Structural and functional analysis of the Pseudomonas aeruginosa PA1677 protein | |||||||||
Components | Cysteine hydrolase | |||||||||
Keywords | UNKNOWN FUNCTION / Pseudomonas aeruginosa / carbon catabolite repression / Crc antagonist | |||||||||
Function / homology | streptothricin hydrolase / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Hydrolases / hydrolase activity / ACETATE ION / LYSINE / Cysteine hydrolase Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | |||||||||
Authors | Sonnleitner, E. / Brear, P. / Luisi, B.F. / Blasi, U. | |||||||||
Funding support | United Kingdom, Austria, 2items
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Citation | Journal: Front Microbiol / Year: 2023 Title: Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control. Authors: Sonnleitner, E. / Bassani, F. / Cianciulli Sesso, A. / Brear, P. / Lilic, B. / Davidovski, L. / Resch, A. / Luisi, B.F. / Moll, I. / Blasi, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cib.cif.gz | 251.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cib.ent.gz | 199.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cib_validation.pdf.gz | 498.2 KB | Display | wwPDB validaton report |
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Full document | 8cib_full_validation.pdf.gz | 503.2 KB | Display | |
Data in XML | 8cib_validation.xml.gz | 52 KB | Display | |
Data in CIF | 8cib_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/8cib ftp://data.pdbj.org/pub/pdb/validation_reports/ci/8cib | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22388.492 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: yddQ1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZIR4 #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-LYS / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sodium HEPES; MOPS (acid) 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 0.2M DL-Glutamic acid monohydrate; 0.2M DL Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→122.63 Å / Num. obs: 120918 / % possible obs: 96.2 % / Redundancy: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.107 / Rrim(I) all: 0.285 / Χ2: 0.97 / Net I/σ(I): 6.7 / Num. measured all: 845570 |
Reflection shell | Resolution: 1.78→1.88 Å / % possible obs: 73.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.302 / Num. measured all: 58756 / Num. unique obs: 13457 / CC1/2: 0.416 / Rpim(I) all: 0.643 / Rrim(I) all: 1.462 / Χ2: 0.93 / Net I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→122.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.277 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.113 / 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: 22.632 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→122.63 Å
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Refine LS restraints |
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