+Open data
-Basic information
Entry | Database: PDB / ID: 1l5b | ||||||
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Title | DOMAIN-SWAPPED CYANOVIRIN-N DIMER | ||||||
Components | cyanovirin-N | ||||||
Keywords | ANTIVIRAL PROTEIN / CYANOVIRIN-N / HIV-INACTIVATING / DOMAIN-SWAPPING / GP120 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc ellipsosporum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Barrientos, L.G. / Louis, J.M. / Botos, I. / Mori, T. / Han, Z. / O'Keefe, B.R. / Boyd, M.R. / Wlodawer, A. / Gronenborn, A.M. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures. Authors: Barrientos, L.G. / Louis, J.M. / Botos, I. / Mori, T. / Han, Z. / O'Keefe, B.R. / Boyd, M.R. / Wlodawer, A. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l5b.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l5b.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l5b_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 1l5b_full_validation.pdf.gz | 473.8 KB | Display | |
Data in XML | 1l5b_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1l5b_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/1l5b ftp://data.pdbj.org/pub/pdb/validation_reports/l5/1l5b | HTTPS FTP |
-Related structure data
Related structure data | 1l5eC 3ezmS 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: 11022.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P81180 #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-NHE / | #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: 3.23 Å3/Da / Density % sol: 61.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 10.3 Details: sodium citrate, CHES, pH 10.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2001 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 16831 / Num. obs: 15588 / % possible obs: 76.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 2→2.13 Å / % possible all: 87.8 |
Reflection | *PLUS Highest resolution: 2.07 Å / Num. obs: 20437 / % possible obs: 99.4 % / Num. measured all: 392421 |
Reflection shell | *PLUS Lowest resolution: 2.07 Å / % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EZM Resolution: 2→19.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1076002.84 / 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: 72.2724 Å2 / ksol: 0.342024 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.237 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.237 / Highest resolution: 2.07 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.406 |