+Open data
-Basic information
Entry | Database: PDB / ID: 3lly | ||||||
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Title | Crystal Structure Analysis of Maclura pomifera agglutinin | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / Maclura pomifera agglutinin / MPA / Lectin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Maclura pomifera (Osage orange) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Huang, J. / Xu, Z. / Wang, D. / Ogato, C. / Hirama, T. / Palczewski, K. / Hazen, S.L. / Lee, X. / Young, N.M. | ||||||
Citation | Journal: Glycobiology / Year: 2010 Title: Characterization of the secondary binding sites of Maclura pomifera agglutinin by glycan array and crystallographic analyses. Authors: Huang, J. / Xu, Z. / Wang, D. / Ogata, C.M. / Palczewski, K. / Lee, X. / Young, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lly.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lly.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3lly ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3lly | HTTPS FTP |
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-Related structure data
Related structure data | 3llzC 3lm1C 1jotS 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: 14768.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: from the seeds of the Moraceae plant family / Source: (natural) Maclura pomifera (Osage orange) / References: UniProt: P18674 |
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#2: Protein/peptide | Mass: 1672.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: from the seeds of the Moraceae plant family / Source: (natural) Maclura pomifera (Osage orange) / References: UniProt: P18676 |
#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: 50.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.5M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the reservoir solution. The sitting drop is made by protein (28mg/mL) and equal volumn of ...Details: 0.5M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the reservoir solution. The sitting drop is made by protein (28mg/mL) and equal volumn of reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 30, 2000 / Details: mirrors |
Radiation | Monochromator: KOHZU double crystal monochromator with a sagittally focused second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. all: 8637 / Num. obs: 7981 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 35.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 14.6 / Num. unique all: 837 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JOT Resolution: 2.25→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 111.6 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.86 Å2 / Biso mean: 26.439 Å2 / Biso min: 9.22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å
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Xplor file |
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