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Yorodumi- PDB-4lsb: Crystal structure of a putative lyase/mutase from Burkholderia ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lsb | ||||||
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Title | Crystal structure of a putative lyase/mutase from Burkholderia cenocepacia J2315 | ||||||
Components | lyase/mutase | ||||||
Keywords | LYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / mutase / cystic fibrosis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of a putative lyase/mutase from Burkholderia cenocepacia J2315 Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lsb.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lsb.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lsb_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 4lsb_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 4lsb_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 4lsb_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4lsb ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4lsb | HTTPS FTP |
-Related structure data
Related structure data | 2ze3S 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 | Mass: 30891.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BceJ2315_55920, BCAM2155 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EFV2 #2: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 8000, 0.2M MgCl2, Tris HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9798 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 48518 / % possible obs: 97.2 % / Redundancy: 5 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4.97 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3583 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZE3 Resolution: 1.8→47.33 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.69 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.121 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.274 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.33 Å
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Refine LS restraints |
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