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Yorodumi- PDB-3lg3: 1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lg3 | ||||||
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Title | 1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92 | ||||||
Components | Isocitrate lyase | ||||||
Keywords | LYASE / Isocitrate Lyase / Conserved / CD / Proteomics evidence (Cytoplasmid or periplasmic) / Drug target functions / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Sharma, S.S. / Brunzelle, J.S. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92 Authors: Sharma, S.S. / Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Savchenko, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lg3.cif.gz | 360.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lg3.ent.gz | 304.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lg3_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 3lg3_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 3lg3_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 3lg3_validation.cif.gz | 65.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/3lg3 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/3lg3 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48186.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: aceA, y0016, YPO3725, YP_3087 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(de3) Ril References: UniProt: Q7CLE1, UniProt: A0A2S9PCG6*PLUS, isocitrate lyase #2: Water | ChemComp-HOH / | |
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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: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M LiCitrate, PEG3350 20%, 10mm iso Citric acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 7, 2009 / Details: Be Lenes |
Radiation | Monochromator: Single Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 185843 / Num. obs: 185843 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.86 / Num. unique all: 9150 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→24.558 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / 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: 36.003 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→24.558 Å
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Refine LS restraints |
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LS refinement shell |
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