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- PDB-2y7f: 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: 2y7f | ||||||
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Title | Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the substrate 3- keto-5-aminohexanoate | ||||||
![]() | 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. THE SHEETS PRESENTED AS "CA" 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 "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-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 | ![]() | 438.1 KB | Display | ![]() |
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PDB format | ![]() | 361.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 461.3 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 70.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y7dSC ![]() 2y7eC ![]() 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 31087.818 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PCRT7/CT-TOPO / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-KMH / ( #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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 30% PEG4000, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 20, 2009 / 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: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→34.39 Å / Num. obs: 101452 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.93 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y7D Resolution: 1.75→33.5 Å / Cor.coef. Fo:Fc: 0.9607 / Cor.coef. Fo:Fc free: 0.9565 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.093 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN KAH MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9400. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN KAH MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9400. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=40. NUMBER TREATED BY BAD NON- BONDED CONTACTS=5.
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Displacement parameters | Biso mean: 20.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.158 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→33.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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