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Yorodumi- PDB-3vfl: Structure, Function, Stability and Knockout Phenotype of Dihydrod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vfl | |||||||||
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Title | Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae | |||||||||
Components | Dihydrodipicolinate synthase | |||||||||
Keywords | LYASE / Dihydrodipicolinate synthase / Lysine Biosynthesis | |||||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : / : Function and homology information | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å | |||||||||
Authors | Gorman, M.A. | |||||||||
Citation | Journal: To be Published Title: Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae Authors: Dogovski, C. / Gorman, M.A. / Ketaren, N.E. / Praszkier, J. / Bryant, G. / Yang, J. / Griffin, M.D.W. / Pearce, F.G. / Bhargava, S.K. / Dobson, R.C.J. / Hutton, C.A. / Gerrard, J.A. / Robins- ...Authors: Dogovski, C. / Gorman, M.A. / Ketaren, N.E. / Praszkier, J. / Bryant, G. / Yang, J. / Griffin, M.D.W. / Pearce, F.G. / Bhargava, S.K. / Dobson, R.C.J. / Hutton, C.A. / Gerrard, J.A. / Robins-Browne, R.M. / Jameson, G.B. / Parker, M.W. / Perugini, M.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization of dihydrodipicolinate synthase from a clinical isolate of Streptococcus pneumoniae. Authors: Sibarani, N.E. / Gorman, M.A. / Dogovski, C. / Parker, M.W. / Perugini, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vfl.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vfl.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vfl_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 3vfl_full_validation.pdf.gz | 483.7 KB | Display | |
Data in XML | 3vfl_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 3vfl_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfl ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfl | HTTPS FTP |
-Related structure data
Related structure data | 4fhaC 3hijS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 2 - 296 / Label seq-ID: 2 - 296
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-Components
#1: Protein | Mass: 33946.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: A5LD17 / Gene: CGSSp3BS71_00085, dapA / Plasmid: pET101/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5LD17, dihydrodipicolinate synthase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M ammonium chloride, 20% (w/v) PEG 6000, 0.1M MES pH 6.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 16, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.91→74.55 Å / Num. obs: 54089 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.061 / Net I/σ(I): 35.73 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HIJ Resolution: 1.91→47.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.694 / SU ML: 0.101 / SU R Cruickshank DPI: 0.0264 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 29.146 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→47.83 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 1.912→1.962 Å / Total num. of bins used: 20
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