+Open data
-Basic information
Entry | Database: PDB / ID: 4jz8 | ||||||
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Title | Carbamate kinase from Giardia lamblia bound to citric acid | ||||||
Components | Carbamate kinase | ||||||
Keywords | TRANSFERASE / modified Rossmann fold / ATP carbamate phosphotransferase / ADP / Mg2+ / carbamoyl phosphate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Giardia lamblia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lim, K. / Herzberg, O. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP. Authors: Lim, K. / Kulakova, L. / Galkin, A. / Herzberg, O. #1: 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 | 4jz8.cif.gz | 254.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jz8.ent.gz | 205.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jz8_validation.pdf.gz | 489.4 KB | Display | wwPDB validaton report |
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Full document | 4jz8_full_validation.pdf.gz | 534.2 KB | Display | |
Data in XML | 4jz8_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 4jz8_validation.cif.gz | 80.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/4jz8 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/4jz8 | HTTPS FTP |
-Related structure data
Related structure data | 4jz7C 4jz9C 2we4S 3kzfS 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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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 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / Gene: GL50803_16453 / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: A8BB85, carbamate kinase #2: Chemical | ChemComp-CIT / #3: 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: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.4 M ammonium citrate dibasic, pH 5.0, 21% PEG3350, crystal soaked in 2 mM inhibitor disulfiram (inhibitor did not bind but unit cell dimension b shrank by 6%), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2011 / 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: 2.1→46.3 Å / Num. all: 67363 / Num. obs: 67363 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3970 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3KZF AND 2WE4 Resolution: 2.1→46.3 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å
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