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Yorodumi- PDB-3plx: The crystal structure of aspartate alpha-decarboxylase from Campy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3plx | |||||||||
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Title | The crystal structure of aspartate alpha-decarboxylase from Campylobacter jejuni subsp. jejuni NCTC 11168 | |||||||||
Components | (Aspartate 1-decarboxylase) x 2 | |||||||||
Keywords | LYASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / double-psi beta-barrel | |||||||||
Function / homology | Function and homology information alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Campylobacter jejuni subsp. jejuni (Campylobacter) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å | |||||||||
Authors | Tan, K. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: To be Published Title: The crystal structure of aspartate alpha-decarboxylase from Campylobacter jejuni subsp. jejuni NCTC 11168 Authors: Tan, K. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3plx.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3plx.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 3plx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/3plx ftp://data.pdbj.org/pub/pdb/validation_reports/pl/3plx | HTTPS FTP |
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-Related structure data
Related structure data | 2c45S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3007.490 Da / Num. of mol.: 1 / Fragment: UNP residues 1-24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0296c, panD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9PIK3, aspartate 1-decarboxylase |
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#2: Protein | Mass: 11255.597 Da / Num. of mol.: 1 / Fragment: UNP residues 25-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0296c, panD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9PIK3, aspartate 1-decarboxylase |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
Compound details | THE PROTEIN IS SELF-PROCESSED AT GLY24-SER25. THE SER25 IS CONVERTED INTO A PYRUVOYL GROUP. |
Sequence details | THE PROTEIN IS SELF-PROCESSED AT GLY24-SER25. THE SER25 IS CONVERTED INTO A PYRUVOYL GROUP. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Sodium Acetate, 0.1M HEPES:NaOH, 20% (W/V) PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2010 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→32 Å / Num. all: 16734 / Num. obs: 16734 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 4.97 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C45 Resolution: 1.747→31.111 Å / SU ML: 0.17 / σ(F): 0.16 / Phase error: 14.08 / 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 / Bsol: 37.132 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.747→31.111 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.4271 Å / Origin y: 13.6452 Å / Origin z: 29.8093 Å
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Refinement TLS group | Selection details: chain A or chain B |