+Open data
-Basic information
Entry | Database: PDB / ID: 2rp3 | ||||||
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Title | Solution Structure of Cyanovirin-N Domain B Mutant | ||||||
Components | Cyanovirin-N | ||||||
Keywords | ANTIVIRAL PROTEIN / CYANOVIRIN-N / HIV-INACTIVATING / GP120 / MONOMER / NO 3D DOMAIN-SWAPPING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc ellipsosporum (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
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 | 2rp3.cif.gz | 565.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rp3.ent.gz | 489.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/2rp3 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/2rp3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10693.746 Da / Num. of mol.: 1 / Mutation: E41A, N42A, P51G, 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE INITIAL STRUCTURES WERE OBTAINED USING CYANA AUTOMATIC CALCULATION, BASED ON CHEMICAL SHIFT LISTS FROM SEQUENCE-SPECIFIC RESONANCE ASSIGNMENT AND NOES FROM 15N AND 13C-EDITED 3D-NOESY ...Text: THE INITIAL STRUCTURES WERE OBTAINED USING CYANA AUTOMATIC CALCULATION, BASED ON CHEMICAL SHIFT LISTS FROM SEQUENCE-SPECIFIC RESONANCE ASSIGNMENT AND NOES FROM 15N AND 13C-EDITED 3D-NOESY SPECTRA. THROUGHOUT ALL CALCULATIONS, 126 BACKBONE TORSION ANGLE CONSTRAINTS DERIVED FROM TALOS, WERE EMPLOYED. CNS WAS USED FOR FURTHER REFINEMENT, USING THE DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS OBTAINED FROM THE FINAL CYCLE OF THE CYANA CALCULATION, AND SEVERAL ADDITIONAL NOE CONSTRAINTS FROM MANUAL CHECKING OF THE 3D NOESY DATA. IN TOTAL, 2076 EXPERIMENTAL NOE-RESTRAINTS (~20 PER RESIDUE) WERE EMPLOYED. FROM NOE-DERIVED ENSEMBLE OF 50 STRUCTURES THE 20 LOWEST ENERGY STRUCTURES WERE FURTHER REFINED AGAINST 15N-1H RESIDUAL DIPOLAR COUPLINGS (62) WITH THE PROGRAM DYNAMO INCLUDED IN THE NMRPIPE PACKAGE. |
-Sample preparation
Details | Contents: 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | pH: 6.0 / Pressure: atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: BRUKER DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: BACKBONE NH DIPOLAR COUPLINGS, RMS=0.64HZ | |||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1 |