+Open data
-Basic information
Entry | Database: PDB / ID: 1zhq | ||||||
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Title | Crystal structure of apo MVL | ||||||
Components | mannan-binding lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / HIV-1 / MVL / cyanobacteria / carbohydrate binding | ||||||
Function / homology | Function and homology information regulation of defense response to virus / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, acting on glycosyl bonds / metabolic process / carbohydrate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Microcystis viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.9 Å | ||||||
Authors | Williams, D.C. / Lee, J.Y. / Cai, M. / Bewley, C.A. / Clore, G.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structures of the HIV-1 Inhibitory Cyanobacterial Protein MVL Free and Bound to Man3GlcNAc2: STRUCTURAL BASIS FOR SPECIFICITY AND HIGH-AFFINITY BINDING TO THE CORE PENTASACCHARIDE FROM ...Title: Crystal Structures of the HIV-1 Inhibitory Cyanobacterial Protein MVL Free and Bound to Man3GlcNAc2: STRUCTURAL BASIS FOR SPECIFICITY AND HIGH-AFFINITY BINDING TO THE CORE PENTASACCHARIDE FROM N-LINKED OLIGOMANNOSIDE. Authors: Williams, D.C. / Lee, J.Y. / Cai, M. / Bewley, C.A. / Clore, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zhq.cif.gz | 198.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zhq.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/1zhq ftp://data.pdbj.org/pub/pdb/validation_reports/zh/1zhq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12244.663 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis viridis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHG4 #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-EDO / #4: 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: 2.401 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Ammonium dihydrogen phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2005 |
Radiation | Monochromator: GRAPHITE / 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→50 Å / Num. all: 73335 / Num. obs: 71428 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.25 / Num. unique all: 6946 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→19.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 460807.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.0686 Å2 / ksol: 0.368284 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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