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Yorodumi- PDB-7ubz: Chymotrypsin digested toxin/immunity complex for a T6SS lipase ef... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ubz | ||||||
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Title | Chymotrypsin digested toxin/immunity complex for a T6SS lipase effector from E. cloacae | ||||||
Components |
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Keywords | TOXIN/IMMUNE SYSTEM / lipase / toxin / immunity / methylglyoxal / TOXIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Alpha/Beta hydrolase fold / CITRATE ANION / methylglyoxal / Uncharacterized protein / : Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Cuthbert, B.J. / Jensen, S.J. / Goulding, C.W. / Hayes, C.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Toxin/immunity complex for a T6SS lipase effector from E. cloacae Authors: Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ubz.cif.gz | 212.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ubz.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 7ubz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ubz_validation.pdf.gz | 1008.2 KB | Display | wwPDB validaton report |
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Full document | 7ubz_full_validation.pdf.gz | 1021.4 KB | Display | |
Data in XML | 7ubz_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 7ubz_validation.cif.gz | 70.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/7ubz ftp://data.pdbj.org/pub/pdb/validation_reports/ub/7ubz | HTTPS FTP |
-Related structure data
Related structure data | 7uc0 S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 25497.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: I6L61_16350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8F3KJ65 #2: Protein | Mass: 33826.016 Da / Num. of mol.: 2 / Fragment: UNP residues 172-472 Source method: isolated from a genetically manipulated source Details: Treated with chymotrypsin during crystallization / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: NCTC10005_04014 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M7ENE2 |
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-Non-polymers , 4 types, 1142 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FLC / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.25 M sodium citrate, 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→38.88 Å / Num. obs: 130201 / % possible obs: 99.1 % / Redundancy: 37.1 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.02 / Rrim(I) all: 0.121 / Net I/σ(I): 23.2 / Num. measured all: 4829779 / Scaling rejects: 2012 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 29.3 % / Rmerge(I) obs: 2.725 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5526 / CC1/2: 0.733 / Rpim(I) all: 0.497 / Rrim(I) all: 2.772 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7UC0 7uc0 Resolution: 1.75→38.76 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 252.18 Å2 / Biso mean: 33.335 Å2 / Biso min: 15.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→38.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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