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Yorodumi- PDB-2eeo: Crystal Structure of T.th. HB8 L-Aspartate-alpha-Decarboxylase Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eeo | |||||||||
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Title | Crystal Structure of T.th. HB8 L-Aspartate-alpha-Decarboxylase Complexed with Fumarate | |||||||||
Components | (Aspartate 1-decarboxylase) x 2 | |||||||||
Keywords | LYASE / Pyruvoyl group dependent enzyme | |||||||||
Function / homology | Function and homology information alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Goto, M. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of T.th. HB8 L-Aspartate-alpha-Decarboxylase Authors: Goto, M. / Omi, R. / Nakajima, O. / Miyahara, I. / Hirotsu, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eeo.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eeo.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 2eeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eeo_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 2eeo_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 2eeo_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2eeo_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2eeo ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2eeo | HTTPS FTP |
-Related structure data
Related structure data | 1vc3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2817.360 Da / Num. of mol.: 1 / Fragment: Aspartate 1-decarboxylase beta chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKN7, aspartate 1-decarboxylase |
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#2: Protein | Mass: 10225.583 Da / Num. of mol.: 1 / Fragment: Aspartate 1-decarboxylase alpha chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKN7, aspartate 1-decarboxylase |
#3: Chemical | ChemComp-PYR / |
#4: Chemical | ChemComp-FUM / |
#5: Water | ChemComp-HOH / |
Sequence details | 25TH RESIDUE IN CHAIN B, SER WAS MODIFIED WITH PYR. REFER TO MOD_RES OF FEATURES IN DATABASE, PAND_THET8. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Na-,K-tartrate, Hepes-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 27, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.17 Å / Num. all: 14772 / Num. obs: 14405 / % possible obs: 97.3 % / Biso Wilson estimate: 13.9 Å2 |
Reflection shell | Resolution: 1.6→1.65 Å / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1VC3 Resolution: 1.6→24.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1257259.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.63 Å2 / ksol: 0.389282 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→24.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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