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- PDB-1n02: Solution Structure of a Circular-Permuted Variant of the Potent H... -

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Basic information

Entry
Database: PDB / ID: 1n02
TitleSolution Structure of a Circular-Permuted Variant of the Potent HIV-inactivating Protein Cyanovirin-N
ComponentsCyanovirin-N
KeywordsViral protein inhibitor / VIRUS/VIRAL PROTEIN INHIBITOR
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 / for dyana, Standard target function-simulated annealing protocol. For CNS, Simulated-annealing in Cartesian space
Model type detailsminimized average
AuthorsBarrientos, L.G. / Gronenborn, A.M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution Structure of a Circular-Permuted Variant of the Potent HIV-inactivating Protein Cyanovirin-N: Structural Basis for Protein Stability and Oligosaccharide Interaction
Authors: Barrientos, L.G. / Louis, J.M. / Ratner, D.M. / Seeberger, P.H. / Gronenborn, A.M.
History
DepositionOct 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _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)11,0791
Polymers11,0791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / -
RepresentativeModel #1minimized average structure

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Components

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


Mass: 11079.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: circular-permuted variant / Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P81180

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
1211H-13C HMQC
131HNHA
141(H)CCH-TOCSY
151(H)C(CCO)NH-TOCSY
161NOESY
1714D 13C/13C separated NOE HNHB
1812D HN(CO)CG
191HNCG
NMR detailsText: The minimized average structure is model 1. Models 2-26 are the the final 25 conformer ensemble. DYANA and CNS were used for refinement. VIRTUALLY COMPLETE RESONANCE ASSIGNMENTS WERE REPORTED I ...Text: The minimized average structure is model 1. Models 2-26 are the the final 25 conformer ensemble. DYANA and CNS were used for refinement. VIRTUALLY COMPLETE RESONANCE ASSIGNMENTS WERE REPORTED I (2001) J.Biom.NMR, 19: 289-90; http://www.bmrb.wisc.edu. Stereo-specific assignments for all the methyl groups of of the eight Leu residues and for the alpha-methylene pr eight Gly, 46 beta-methylene protons and the gamma-methy of the seven Ile were available. In total, 1879 experim were employed, representing ~19 constraints per residue. structures was first calculated with DYANA, based on 114 92 hydrogen bond distances and 193 dihedral angles. Ref values yielded an esemble of 50 structures exhibiting at 0.26+/-0.06 A and 0.64+/-0.08A with respect to the mean backbone (N,CA,C') and all heavy atoms, respectively, an 0.81+/-0.10A^2. This initial ensemble of structures was residual dipolar couplings (80) and chemical shifts (291 programs CNS. Overall, excellent agreement with the exp good covalent geometry was maintained throughout. The f was selected and are presented here as MODELS2-26, and a mean structure of this ensemble is presented here as MOD.

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Sample preparation

Sample conditionspH: 6.0 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DRX600BrukerDRX6006002
Bruker DMX750BrukerDMX7507503
Bruker DMX800BrukerDMX8008004

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Processing

NMR software
NameDeveloperClassification
DYANAGuntert, Mumenthaler, Wuthrichrefinement
DYANAstructure solution
CNSstructure solution
RefinementMethod: for dyana, Standard target function-simulated annealing protocol. For CNS, Simulated-annealing in Cartesian space
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 26

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