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- PDB-2y7e: Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y7e | ||||||
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Title | Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus Cloacamonas acidaminovorans (tetragonal form) | ||||||
![]() | 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME | ||||||
![]() | LYASE / ALDOLASE | ||||||
Function / homology | ![]() 3-keto-5-aminohexanoate cleavage enzyme / 3-keto-5-aminohexanoate cleavage activity / L-lysine catabolic process to acetate / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bellinzoni, M. / Alzari, P.M. | ||||||
![]() | ![]() Title: 3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold for an Uncommon Claisen-Type Condensation. Authors: Bellinzoni, M. / Bastard, K. / Perret, A. / Zaparucha, A. / Perchat, N. / Vergne, C. / Wagner, T. / De Melo-Minardi, R.C. / Artiguenave, F. / Cohen, G.N. / Weissenbach, J. / Salanoubat, M. / Alzari, P.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.3 KB | Display | ![]() |
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PDB format | ![]() | 188.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y7dSC ![]() 2y7fC ![]() 2y7gC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.0043, 0.9902, 0.1395), Vector: |
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Components
#1: Protein | Mass: 31087.818 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PCRT7/CT-TOPO / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.2 % / Description: NONE |
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Crystal grow | pH: 7 Details: 20% PEG3350, 0.220 M MG FORMATE, 26.4% GLYCEROL, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 22, 2010 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→50 Å / Num. obs: 133532 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.28→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y7D Resolution: 1.28→45.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.145 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.113 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→45.76 Å
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Refine LS restraints |
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