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Yorodumi- PDB-3c4u: Structure of class II fructose-biphosphate aldolase from helicoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4u | ||||||
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Title | Structure of class II fructose-biphosphate aldolase from helicobacter pylori | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / FBP aldolase / Class II / ZINC / glycolysis / Metal-binding | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å | ||||||
Authors | Coincon, M. / Sygusch, J. | ||||||
Citation | Journal: Chemistry / Year: 2008 Title: Synthesis and Biochemical Evaluation of Selective Inhibitors of Class II Fructose Bisphosphate Aldolases: Towards New Synthetic Antibiotics. Authors: Fonvielle, M. / Coincon, M. / Daher, R. / Desbenoit, N. / Kosieradzka, K. / Barilone, N. / Gicquel, B. / Sygusch, J. / Jackson, M. / Therisod, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c4u.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4u.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c4u_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 3c4u_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 3c4u_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 3c4u_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4u ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4u | HTTPS FTP |
-Related structure data
Related structure data | 3c52C 3c56C 1rvgS 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
#1: Protein | Mass: 33800.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fba / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P56109, fructose-bisphosphate aldolase #2: Chemical | #3: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.58 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. all: 72445 / Num. obs: 71999 / % possible obs: 99.4 % / Redundancy: 8.64 % / Biso Wilson estimate: 10.93 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.245 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.62→1.68 Å / Mean I/σ(I) obs: 6.4 / Num. unique all: 7031 / Rsym value: 0.697 / % possible all: 0.983 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1RVG Resolution: 1.83→33.404 Å / FOM work R set: 0.824 / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: ML / Details: The Friedel pairs were used in phasing
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.259 Å2 / ksol: 0.379 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 1.27 Å2 / Biso mean: 17.42 Å2 / Biso min: 70.69 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→33.404 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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