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Yorodumi- PDB-4mg4: Crystal structure of a putative phosphonomutase from Burkholderia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mg4 | ||||||
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Title | Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315 | ||||||
Components | Phosphonomutase | ||||||
Keywords | UNKNOWN FUNCTION / SSGCID / NIAID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia cenocepacia J2315 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315 Authors: Lukacs, C.M. / Edwards, T.E. / Lorimer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mg4.cif.gz | 743.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mg4.ent.gz | 614.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/4mg4 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/4mg4 | HTTPS FTP |
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-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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Unit cell |
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-Components
#1: Protein | Mass: 27699.352 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria) Strain: J2315 / Gene: BceJ2315_40480, BCAM0587 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EL08 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / #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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 Details: JCSG+c2: 20% PEG6000, 1M LiCl, 0.1M NaCit pH4.0, 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: RAYONIX MX-300 / 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: 1.7→50 Å / Num. all: 236885 / Num. obs: 236354 / % possible obs: 99.8 % / Redundancy: 3.76 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.15 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.51 / Num. unique all: 17451 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZE3 Resolution: 1.7→46.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.192 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / 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: 21.112 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→46.29 Å
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Refine LS restraints |
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