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- PDB-2rp3: Solution Structure of Cyanovirin-N Domain B Mutant -

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Basic information

Entry
Database: PDB / ID: 2rp3
TitleSolution Structure of Cyanovirin-N Domain B Mutant
ComponentsCyanovirin-N
KeywordsANTIVIRAL PROTEIN / CYANOVIRIN-N / HIV-INACTIVATING / GP120 / MONOMER / NO 3D DOMAIN-SWAPPING
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc ellipsosporum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMatei, E. / Furey, W. / Gronenborn, A.M.
CitationJournal: 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
DepositionApr 30, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)10,6941
Polymers10,6941
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cyanovirin-N / / CV-N


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D 15N-NOESY HSQC
16113C-NOESY
NMR detailsText: 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.

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Sample preparation

DetailsContents: 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMCVNmutDB-1[U-100% 15N]1
1.5 mMCVNmutDB-2[U-100% 13C; U-100% 15N]1
Sample conditionspH: 6.0 / Pressure: atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: BRUKER DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAHERRMANN, GUNTERT, WUTHRICHrefinement
CNSBRUNGER, ADAMS, CLORE, DELANO, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
TopSpinBruker Biospinstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRViewJohnson, One Moon Scientificstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
DYNAMO(NMRpipe)Cornilescu, Delaglio and Baxstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: BACKBONE NH DIPOLAR COUPLINGS, RMS=0.64HZ
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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