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Yorodumi- PDB-3eol: 2.0A crystal structure of isocitrate lyase from Brucella melitens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eol | ||||||
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Title | 2.0A crystal structure of isocitrate lyase from Brucella melitensis (P43212) | ||||||
Components | isocitrate lyase | ||||||
Keywords | LYASE / BRUCELLA / MELITENSIS / ISOCITRATE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID | ||||||
Function / homology | Function and homology information isocitrate lyase / glyoxysome / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structures of isocitrate lyase from Brucella melitensis Authors: SSGCID | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eol.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eol.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 3eol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eol_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 3eol_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 3eol_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 3eol_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/3eol ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eol | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47206.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: BMEI0409 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8YIN4, UniProt: Q2YQA0*PLUS, isocitrate lyase #2: Chemical | ChemComp-GOL / | #3: Chemical | #4: 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: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: 20% PEG 8000, 0.05M KH2PO4, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→39.84 Å / Num. obs: 62451 / % possible obs: 99.9 % / Redundancy: 6.64 % / Rmerge(I) obs: 0.156 / Χ2: 0.97 / Scaling rejects: 3133 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 49.74 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.237 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.814 / SU B: 4.652 / SU ML: 0.13 / SU R Cruickshank DPI: 0.182 / SU Rfree: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.16 Å2 / Biso mean: 37.863 Å2 / Biso min: 23.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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