+Open data
-Basic information
Entry | Database: PDB / ID: 3czz | ||||||
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Title | Crystal structure of Cyanovirin-N domain B mutant | ||||||
Components | Cyanovirin-N | ||||||
Keywords | ANTIVIRAL PROTEIN / CYANOVIRIN-N / SUGAR BINDING PROTEIN / HIV-INACTIVATING / GP120 / Protein synthesis inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc ellipsosporum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Matei, E. / Furey, W. / Gronenborn, A.M. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Solution and crystal structures of a sugar binding site mutant of cyanovirin-N: no evidence of domain swapping. Authors: Matei, E. / Furey, W. / 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 | 3czz.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3czz.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 3czz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3czz_validation.pdf.gz | 403.4 KB | Display | wwPDB validaton report |
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Full document | 3czz_full_validation.pdf.gz | 403.5 KB | Display | |
Data in XML | 3czz_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3czz_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3czz ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czz | HTTPS FTP |
-Related structure data
Related structure data | 2rp3C 1l5bS 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: 10693.746 Da / Num. of mol.: 2 / Mutation: E41A, N42A, T57A, R76A, Q78G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Plasmid: PET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81180 #2: 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: 2.04 Å3/Da / Density % sol: 39.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M AMMONIUM ACETATE, 24% POLYETHYLE MONOMETYL ETHER, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 14, 2007 / Details: HF VariMax |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→29.01 Å / Num. obs: 37884 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.43 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.36→1.41 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.5 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L5B Resolution: 1.36→29.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 995851.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 250 Å2 / ksol: 0.68 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.36→29.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.45 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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