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- PDB-2jzl: Structure of NcCVNH (N. CRASSA CVNH) -

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Basic information

Entry
Database: PDB / ID: 2jzl
TitleStructure of NcCVNH (N. CRASSA CVNH)
ComponentsCyanovirin-N homolog
KeywordsCarbohydrate binding protein / CVNH / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


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
Cyanovirin-N homolog
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsKoharudin, L.M.I. / Viscomi, A.R. / Jee, J. / Ottonello, S. / Gronenborn, A.M.
CitationJournal: Structure / Year: 2008
Title: The evolutionarily conserved family of cyanovirin-N homologs: structures and carbohydrate specificity.
Authors: Koharudin, L.M. / Viscomi, A.R. / Jee, J.G. / Ottonello, S. / Gronenborn, A.M.
History
DepositionJan 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct.title
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Cyanovirin-N homolog


Theoretical massNumber of molelcules
Total (without water)13,2211
Polymers13,2211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 800structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cyanovirin-N homolog / Cyanovirin-N-like protein


Mass: 13221.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7S6U4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HN(CA)CB
1423D (H)CCH-TOCSY
1523D H(CCO)NH
1623D H(CCO)NH
17215N-NOESY HSQC
18213C-NOESY HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 15N] NcCVNH, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] NcCVNH, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMNcCVNH[U-100% 15N]1
20 mMsodium phosphate1
0.02 %sodium azide1
1.0 mMNcCVNH[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
0.02 %sodium azide2
Sample conditionspH: 6 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TALOSCornilescu, Delaglio and Baxiterative matrix relaxation
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SA using CNS followed by explicit water refinement implemenetd in ARIA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 800 / Conformers submitted total number: 30

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