+Open data
-Basic information
Entry | Database: PDB / ID: 2rdk | |||||||||
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Title | Five site mutated Cyanovirin-N with Mannose dimer bound | |||||||||
Components | Cyanovirin-N | |||||||||
Keywords | ANTIVIRAL PROTEIN / Cyanovirin-N / sugar binding protein / anti HIV / Protein synthesis inhibitor | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Nostoc ellipsosporum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Fromme, R. / Katiliene, Z. / Fromme, P. / Ghirlanda, G. | |||||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution. Authors: Fromme, R. / Katiliene, Z. / Fromme, P. / Ghirlanda, G. #1: Journal: Biochemistry / Year: 2007 Title: A monovalent mutant of cyanovirin-n provides insight into the role of multiple interactions with gp120 for antiviral activity. Authors: Fromme, R. / Katiliene, Z. / Giomarelli, B. / Bogani, F. / Mc Mahon, J. / Mori, T. / Fromme, P. / Ghirlanda, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rdk.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rdk.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 2rdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/2rdk ftp://data.pdbj.org/pub/pdb/validation_reports/rd/2rdk | HTTPS FTP |
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-Related structure data
Related structure data | 2pysS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 20 - 30 / Label seq-ID: 20 - 30
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-Components
#1: Protein | Mass: 11949.095 Da / Num. of mol.: 2 / Mutation: K3N T7A E23I N93A P51G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): M51 / References: UniProt: P81180 #2: Polysaccharide | #3: 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: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 30% PEG 8000, 100 MM MGSO4, 2 MM MAN2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→48.45 Å / Num. obs: 43019 / % possible obs: 94.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.97 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PYS Resolution: 1.35→8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.059 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 81 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.35→1.38 Å / Total num. of bins used: 20
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