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Yorodumi- PDB-1kxv: Camelid VHH Domains in Complex with Porcine Pancreatic alpha-Amylase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kxv | ||||||
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Title | Camelid VHH Domains in Complex with Porcine Pancreatic alpha-Amylase | ||||||
Components |
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Keywords | HYDROLASE / IMMUNE SYSTEM / BETA 8 ALPHA 8 / BETA BARREL | ||||||
Function / homology | Function and homology information alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Camelus dromedarius (Arabian camel) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Desmyter, A. / Spinelli, S. / Payan, F. / Lauwereys, M. / Wyns, L. / Muyldermans, S. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology. Authors: Desmyter, A. / Spinelli, S. / Payan, F. / Lauwereys, M. / Wyns, L. / Muyldermans, S. / Cambillau, C. #1: Journal: Embo J. / Year: 1998 Title: Potent enzyme inhibitors derived from dromedary heavy-chain antibodies. Authors: Lauwereys, M. / Arbabi Ghahroudi, M. / Desmyter, A. / Kinne, J. / Holzer, W. / De Genst, E. / Wyns, L. / Muyldermans, S. #2: Journal: J.MOL.BIOL. / Year: 1993 Title: Structure and Molecular Model Refinement of Pig Pancreatic alpha-amylase at 2.1 A Resolution Authors: Qian, M. / Haser, R. / Payan, F. | ||||||
History |
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Remark 999 | SEQUENCE The discrepancy between the sequence of this entry and the database reference is explained ...SEQUENCE The discrepancy between the sequence of this entry and the database reference is explained in reference 2 given above. An appropriate sequence database reference for the antibody CAMELID VHH DOMAIN CAB10 , chains C and D, was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kxv.cif.gz | 280.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kxv.ent.gz | 219.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kxv ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kxv | HTTPS FTP |
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-Related structure data
Related structure data | 1kxqC 1kxtC 1fjhS 1qd0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55462.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PANCEATIC ENZYME / Source: (natural) Sus scrofa (pig) / References: UniProt: P00690, alpha-amylase #2: Antibody | Mass: 12837.308 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: PHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK #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: 2.61 Å3/Da / Density % sol: 52.79 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG4000 32%, Na citrate 0.1M & Ammonium Acetate 0.2M, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2000 / Details: diamond |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 175069 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 2 / % possible all: 95 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / % possible obs: 99.8 % / Num. measured all: 716803 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 99.5 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FJH, PDB ENTRY 1QD0 Resolution: 1.6→29.34 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1228117.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.0628 Å2 / ksol: 0.361799 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Rfactor obs: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / Rfactor obs: 0.228 |