+Open data
-Basic information
Entry | Database: PDB / ID: 4c25 | ||||||
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Title | L-fuculose 1-phosphate aldolase | ||||||
Components | L-FUCULOSE PHOSPHATE ALDOLASE | ||||||
Keywords | LYASE / FUCOSE PROCESSING | ||||||
Function / homology | Function and homology information L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 | 4c25.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c25.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 4c25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/4c25 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/4c25 | HTTPS FTP |
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-Related structure data
Related structure data | 4c20C 4c21C 4c22C 4c23C 4c24C 2fuaS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23545.959 Da / Num. of mol.: 1 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: Q97N89, UniProt: A0A0H2US48*PLUS, L-fuculose-phosphate aldolase |
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-Non-polymers , 7 types, 109 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-NI / | ||||
#4: Chemical | ChemComp-13P / | ||||
#5: Chemical | ChemComp-SO4 / | ||||
#6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
-Details
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: 2.77 Å3/Da / Density % sol: 55.7 % / Description: NONE |
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Crystal grow | pH: 8 Details: SPFCSA AT A CONCENTRATION OF 14 MG PER ML, BUFFERED IN 20 MM TRIS-HCL (PH 8.0) AND 5 MM DITHIOTHREITOL (DTT) WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION OF 4% (V PER V) ...Details: SPFCSA AT A CONCENTRATION OF 14 MG PER ML, BUFFERED IN 20 MM TRIS-HCL (PH 8.0) AND 5 MM DITHIOTHREITOL (DTT) WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION OF 4% (V PER V) GLYCEROL, 1.50 M AMMONIUM SULPHATE, 100 MM TRIS-HCL (PH 8.5) AND 8 MM ZINC CHLORIDE. |
-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 | Resolution: 2.03→40 Å / Num. obs: 15800 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FUA Resolution: 2.03→80.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.778 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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: 38.475 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→80.25 Å
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