+Open data
-Basic information
Entry | Database: PDB / ID: 3s3z | ||||||
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Title | Crystal Structure an Tandem Cyanovirin-N Dimer, CVN2L10 | ||||||
Components | Tandem Cyanovirin-N Dimer CVN2L10 | ||||||
Keywords | ANTIVIRAL PROTEIN / cyanovirin-N / sugar-binding / gp120 / engineered dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc ellipsosporum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Keeffe, J.R. / Bjorkman, P.J. / Mayo, S.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Designed oligomers of cyanovirin-N show enhanced HIV neutralization. Authors: Keeffe, J.R. / Gnanapragasam, P.N. / Gillespie, S.K. / Yong, J. / Bjorkman, P.J. / Mayo, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s3z.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s3z.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s3z_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 3s3z_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 3s3z_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 3s3z_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/3s3z ftp://data.pdbj.org/pub/pdb/validation_reports/s3/3s3z | HTTPS FTP |
-Related structure data
Related structure data | 3s3yC 3ezmS 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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Unit cell |
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Details | Authors state that the biologically relevant molecule is generated by applying the crystallographic symmetry operations Y, X, -Z to the first half of the protein. |
-Components
#1: Protein | Mass: 23999.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81180 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 20% PEG 3350, 0.2 M sodium fluoride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.99984 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→41.56 Å / Num. all: 11158 / Num. obs: 11158 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 12.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EZM Resolution: 1.75→36.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.1993 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.875 / SU B: 2.26 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1209 / SU Rfree: 0.1102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: (1) Only half of the crystallized molecule is in the asymmetric unit. The entire polypeptide chain (biologically relevant molecule) is generated by the operations: Y, X, -Z. (2) Because only ...Details: (1) Only half of the crystallized molecule is in the asymmetric unit. The entire polypeptide chain (biologically relevant molecule) is generated by the operations: Y, X, -Z. (2) Because only half of the biologically relevant molecule is in the asymmetric unit, the density corresponding to residue 0 in the structure is from both an Arg in the expression tag (residue 0 of the sequence) and a Gly from the linker (residue 111 of the sequence). Since side chain density was not seen, the backbone was modeled at 100% occupancy and the side chain was not modeled. (3) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.95 Å2 / Biso mean: 20.3458 Å2 / Biso min: 10.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→36.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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