+Open data
-Basic information
Entry | Database: PDB / ID: 4c23 | ||||||
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Title | L-fuculose kinase | ||||||
Components | L-FUCULOSE KINASE FUCK | ||||||
Keywords | TRANSFERASE / FUCOSE PROCESSING | ||||||
Function / homology | Function and homology information L-fuculokinase / L-fuculokinase activity / rhamnulokinase activity / rhamnose catabolic process Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Higgins, M.A. / Suits, M.D.L. / Marsters, C. / Boraston, A.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structural and Functional Analysis of Fucose-Processing Enzymes from Streptococcus Pneumoniae. Authors: Higgins, M.A. / Suits, M.D. / Marsters, C. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c23.cif.gz | 204.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c23.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 4c23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c23_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 4c23_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 4c23_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 4c23_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/4c23 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/4c23 | HTTPS FTP |
-Related structure data
Related structure data | 4c20C 4c21C 4c22C 4c24C 4c25C 2cgkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53566.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q97N88, UniProt: A0A0H2US93*PLUS, L-fuculokinase #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | Sequence details | POLYPEPTID | |
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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: 2.43 Å3/Da / Density % sol: 49.35 % / Description: NONE |
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Crystal grow | pH: 7.2 Details: SPFCSK AT A CONCENTRATION OF 24 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.2), 150 MM NACL, 1 MM MANGANESE CHLORIDE, AND 1 MM DTT WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION ...Details: SPFCSK AT A CONCENTRATION OF 24 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.2), 150 MM NACL, 1 MM MANGANESE CHLORIDE, AND 1 MM DTT WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION CONSISTING OF 4% (V PER V) ETHYLENE-GLYCOL, 100 MM 4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID (PH 7.5), AND 1.50 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2012 / Details: RH COATED | |||||||||||||||
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→37 Å / Num. obs: 67536 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CGK Resolution: 2→36.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.988 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 31.896 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.98 Å
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