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Yorodumi- PDB-7v8t: Crystal structure of class II pyruvate aldolase from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v8t | ||||||
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Title | Crystal structure of class II pyruvate aldolase from Pseudomonas aeruginosa. | ||||||
Components | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase | ||||||
Keywords | LYASE / Class II pyruvate aldolase / Hexamer / TIM barrel fold | ||||||
Function / homology | Function and homology information 4-hydroxy-2-oxoheptanedioate aldolase / 2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity / phenylacetate catabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Seo, P.W. / Kim, J.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Biochemical and Molecular Characterization of Pyruvate Aldolase for the Synthesis of 2-Keto-4-hydroxybutyrate. Authors: Jeong, Y.J. / Le, T.K. / Seo, P.W. / Ju, S.B. / Kim, J.S. / Yeom, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v8t.cif.gz | 565.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v8t.ent.gz | 466.3 KB | Display | PDB format |
PDBx/mmJSON format | 7v8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/7v8t ftp://data.pdbj.org/pub/pdb/validation_reports/v8/7v8t | HTTPS FTP |
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-Related structure data
Related structure data | 2vwtS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 28230.148 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A081HJP9, 4-hydroxy-2-oxoheptanedioate aldolase #2: Chemical | ChemComp-IOD / #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 200mM sodium iodide, 24% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 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: 2.48→50 Å / Num. obs: 51389 / % possible obs: 96.6 % / Redundancy: 6 % / Biso Wilson estimate: 39.26 Å2 / Rpim(I) all: 0.094 / Rrim(I) all: 0.241 / Rsym value: 0.173 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 2440 / CC1/2: 0.468 / Rpim(I) all: 0.566 / Rsym value: 0.856 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VWT Resolution: 2.48→46.54 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.37 / 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: 115.11 Å2 / Biso mean: 42.2375 Å2 / Biso min: 20.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→46.54 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: -19.1135 Å / Origin y: -19.6095 Å / Origin z: 4.9468 Å
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Refinement TLS group |
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