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Yorodumi- PDB-3c6c: Crystal structure of a putative 3-keto-5-aminohexanoate cleavage ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c6c | ||||||
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Title | Crystal structure of a putative 3-keto-5-aminohexanoate cleavage enzyme (reut_c6226) from ralstonia eutropha jmp134 at 1.72 A resolution | ||||||
Components | 3-keto-5-aminohexanoate cleavage enzyme | ||||||
Keywords | HYDROLASE / Duf849 family protein / tim beta/alpha-barrel fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ralstonia eutropha (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 at 1.72 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c6c.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c6c.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c6c_validation.pdf.gz | 451.6 KB | Display | wwPDB validaton report |
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Full document | 3c6c_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 3c6c_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 3c6c_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/3c6c ftp://data.pdbj.org/pub/pdb/validation_reports/c6/3c6c | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34854.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_293392.1, Reut_C6226 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46MU0 |
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-Non-polymers , 5 types, 397 molecules
#2: Chemical | ChemComp-NI / | ||||
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#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
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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: 2.92 Å3/Da / Density % sol: 57.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: NANODROP, 0.2M Lithium acetate, 20.0% PEG 3350, No Buffer pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97964 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2008 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97964 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→38.72 Å / Num. obs: 43691 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.155 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.72→38.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.669 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.082 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. AN X-RAY EMISSION SPECTRUM AND AN X-RAY FLUORESCENCE SCAN NEAR NI ABSORPTION EDGE TAKEN FROM THE SAMPLE VERIFY THE PRESENCE OF NI METAL. THE OCCUPANCY WAS ADJUSTED TO REFLECT THE DENSITY AND TO PROVIDE A SIMILAR B-FACTOR AS THE COORDINATING PROTEIN ATOMS. 5. EDO, ACT AND PEG FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
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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: 17.493 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→38.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 31.9292 Å / Origin y: 39.8619 Å / Origin z: 49.9412 Å
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