+Open data
-Basic information
Entry | Database: PDB / ID: 4c21 | ||||||
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Title | L-Fucose Isomerase In Complex With Fucitol | ||||||
Components | L-FUCOSE ISOMERASE | ||||||
Keywords | ISOMERASE / FUCOSE PROCESSING | ||||||
Function / homology | Function and homology information arabinose isomerase activity / L-fucose isomerase / L-fucose isomerase activity / D-arabinose catabolic process / L-fucose catabolic process / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c21.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c21.ent.gz | 207 KB | Display | PDB format |
PDBx/mmJSON format | 4c21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c21_validation.pdf.gz | 477.4 KB | Display | wwPDB validaton report |
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Full document | 4c21_full_validation.pdf.gz | 493.3 KB | Display | |
Data in XML | 4c21_validation.xml.gz | 50.5 KB | Display | |
Data in CIF | 4c21_validation.cif.gz | 73.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/4c21 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/4c21 | HTTPS FTP |
-Related structure data
Related structure data | 4c20C 4c22C 4c23C 4c24C 4c25C 1fuiS 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
#1: Protein | Mass: 67825.578 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: Q97N97, L-fucose isomerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | MOLECULE B INCLUDES THE N-TERMINAL TAG | |
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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: 3.44 Å3/Da / Density % sol: 64.27 % / Description: NONE |
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Crystal grow | pH: 8 Details: SPFCSI AT A CONCENTRATION OF 12 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.0), 150 MM NACL, AND 2 MM DTT WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUMES OF 100 MM TRIS-HCL (PH 8.0), 27% (W PER ...Details: SPFCSI AT A CONCENTRATION OF 12 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.0), 150 MM NACL, AND 2 MM DTT WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUMES OF 100 MM TRIS-HCL (PH 8.0), 27% (W PER V) POLYETHYLENE GLYCOL 4,000, 50 MM NACL, AND 200 MM MAGNESIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03318 |
Detector | Type: MARRESEARCH MX-300HE / Detector: CCD / Date: Mar 27, 2012 Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT) |
Radiation | Monochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 59825 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.3 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FUI Resolution: 2.55→49.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.172 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.206 / 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: 33.132 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→49.71 Å
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Refine LS restraints |
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