+Open data
-Basic information
Entry | Database: PDB / ID: 3gak | ||||||
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Title | Structure of Giardia fructose-1,6-biphosphate aldolase | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / Class II fructose-1 / 6-bisphosphate aldolase / glycolytic pathway / Giardia lamblia / drug target / Glycolysis | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Galkin, A. / Herzberg, O. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase. Authors: Galkin, A. / Li, Z. / Li, L. / Kulakova, L. / Pal, L.R. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gak.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gak.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gak_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 3gak_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 3gak_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3gak_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/3gak ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3gak | HTTPS FTP |
-Related structure data
Related structure data | 3gayC 3gb6C 2iswS S: Starting model for refinement C: citing same article (ref.) |
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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: 35263.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: WB / Gene: ald, FBPA / Plasmid: pET100/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: O97447, fructose-bisphosphate aldolase #2: Chemical | #3: Chemical | ChemComp-SO4 / Sequence details | AUTHORS STATE THAT ACCORDING TO THE SEQUENCE FROM GIARDIA GENOME (GB ENTRY EAA46366.1) THE CORRECT ...AUTHORS STATE THAT ACCORDING TO THE SEQUENCE FROM GIARDIA GENOME (GB ENTRY EAA46366.1) THE CORRECT RESIDUE AT POSITION 129 IS GLY. | |
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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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18-25% PEG3350, 0.2M MgSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2007 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→10 Å / Num. all: 14110 / Num. obs: 12210 / % possible obs: 86.6 % / Rmerge(I) obs: 0.114 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.25 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ISW Resolution: 2.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.97 Å /
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