+Open data
-Basic information
Entry | Database: PDB / ID: 1lke | ||||||
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Title | ENGINEERED LIPOCALIN DIGA16 IN COMPLEX WITH DIGOXIGENIN | ||||||
Components | DigA16 | ||||||
Keywords | LIGAND BINDING PROTEIN / PIERIS BRASSICAE / LIPOCALIN / ANTICALIN / GENETICAL ENGINEERING / DIGOXIGENIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pieris brassicae (large cabbage white) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Korndoerfer, I.P. / Skerra, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin. Authors: Korndoerfer, I.P. / Schlehuber, S. / Skerra, A. #1: Journal: J.Mol.Biol. / Year: 2000 Title: A Novel Type of Receptor Protein, based on the Lipocalin Scaffold, with Specificity for Digoxigenin Authors: Schlehuber, S. / Beste, G. / Skerra, A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Small Antibody-like Proteins with Prescribed Ligand Specificities Derived from the Lipocalin Fold. Authors: Beste, G. / Schmidt, F.S. / Stibora, T. / Skerra, A. | ||||||
History |
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Remark 999 | SEQUENCE NWSHPQFEK is the sequence of the Strep-tagII, which the authors used to purify the protein. ...SEQUENCE NWSHPQFEK is the sequence of the Strep-tagII, which the authors used to purify the protein. The extra S before is a linker. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lke.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lke.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lke ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lke | HTTPS FTP |
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-Related structure data
Related structure data | 1kxoC 1lnmC 1bbpS 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: 20833.158 Da / Num. of mol.: 1 Mutation: N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M Source method: isolated from a genetically manipulated source Details: GENETICALLY ENGINEERED VARIANT OF BILIN BINDING PROTEIN Source: (gene. exp.) Pieris brassicae (large cabbage white) / Plasmid: pbbp21-diga16 / Production host: Escherichia coli (E. coli) / Strain (production host): jm83 / References: UniProt: P09464 |
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#2: Chemical | ChemComp-DOG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1-M HEPES, 10% ISOPROPANOL, 19% PEG 4000, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2001 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→99 Å / Num. all: 14294 / Num. obs: 14294 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.06 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 6 / Num. unique all: 1411 / Rsym value: 0.22 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1BBP Resolution: 1.9→48.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.212 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.151 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2 Å / Total num. of bins used: 10
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