+Open data
-Basic information
Entry | Database: PDB / ID: 3kzf | ||||||
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Title | Structure of Giardia Carbamate Kinase | ||||||
Components | Carbamate kinase | ||||||
Keywords | TRANSFERASE / Carbamate kinase / arginine dihydrolase pathway / Giardia lamblia / drug target / Kinase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Giardia lamblia ATCC 50803 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Galkin, A. / Herzberg, O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: X-ray structure and characterization of carbamate kinase from the human parasite Giardia lamblia. Authors: Galkin, A. / Kulakova, L. / Wu, R. / Nash, T.E. / 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 | 3kzf.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzf.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kzf_validation.pdf.gz | 487.7 KB | Display | wwPDB validaton report |
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Full document | 3kzf_full_validation.pdf.gz | 555.2 KB | Display | |
Data in XML | 3kzf_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 3kzf_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzf ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzf | HTTPS FTP |
-Related structure data
Related structure data | 1e19S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33975.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia lamblia ATCC 50803 (eukaryote) / Strain: WB / Gene: CK, GL50803_16453 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: A8BB85, carbamate kinase #2: Chemical | ChemComp-GOL / |
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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: 42.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350 and 0.2 M ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2006 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 23098 / Num. obs: 20419 / % possible obs: 88.4 % / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.193 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1e19 Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: Engh & Huber
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.071 Å / Total num. of bins used: 20
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