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Yorodumi- PDB-3ohi: Structure of Giardia fructose-1,6-biphosphate aldolase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ohi | ||||||
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Title | Structure of Giardia fructose-1,6-biphosphate aldolase in complex with 3-hydroxy-2-pyridone | ||||||
Components | Putative fructose-1,6-bisphosphate aldolase | ||||||
Keywords | LYASE / Class II fructose-1 / 6-bisphosphate aldolase / glycolytic pathway | ||||||
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 | Giardia intestinalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Herzberg, O. / Galkin, A. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2010 Title: Rational design, synthesis and evaluation of first generation inhibitors of the Giardia lamblia fructose-1,6-biphosphate aldolase. Authors: Li, Z. / Liu, Z. / Cho, D.W. / Zou, J. / Gong, M. / Breece, R.M. / Galkin, A. / Li, L. / Zhao, H. / Maestas, G.D. / Tierney, D.L. / Herzberg, O. / Dunaway-Mariano, D. / Mariano, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ohi.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ohi.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ohi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ohi_validation.pdf.gz | 990.3 KB | Display | wwPDB validaton report |
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Full document | 3ohi_full_validation.pdf.gz | 1003.5 KB | Display | |
Data in XML | 3ohi_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 3ohi_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/3ohi ftp://data.pdbj.org/pub/pdb/validation_reports/oh/3ohi | HTTPS FTP |
-Related structure data
Related structure data | 3gayS 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: 35293.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: WB / Gene: ald, FBPA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: O97447, 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: 2.11 Å3/Da / Density % sol: 41.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18-25% Polyethylglycol 3350, 0.2 M NH4NO3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 25998 / Num. obs: 22497 / % possible obs: 86.6 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.248 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GAY Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.772 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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