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- PDB-2l2f: NMR Structure of GzCVNH (Gibberella zeae CVNH) -

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Basic information

Entry
Database: PDB / ID: 2l2f
TitleNMR Structure of GzCVNH (Gibberella zeae CVNH)
ComponentsCyanovirin-N HOMOLOG
KeywordsSUGAR BINDING PROTEIN / Cyanovirin-n homolog / lectin / Carbohydrate binding protein
Function / homologyHIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta / Chromosome 3, complete genome
Function and homology information
Biological speciesGibberella zeae (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average, model 1
AuthorsMatei, E. / Louis, J.M. / Jee, J.G. / Gronenborn, A.M.
CitationJournal: Proteins / Year: 2011
Title: NMR solution structure of a cyanovirin homolog from wheat head blight fungus.
Authors: Matei, E. / Louis, J.M. / Jee, J. / Gronenborn, A.M.
History
DepositionAug 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanovirin-N HOMOLOG


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
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)20 / 50structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein Cyanovirin-N HOMOLOG / CYANOVIRIN-N-LIKE PROTEIN


Mass: 11673.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I1RM03*PLUS

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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 15N-NOESY HSQC
16213C-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,121 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, 2401 EXPERIMENTAL NOE-RESTRAINTS (~20 PER RESIDUE) WERE EMPLOYED.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 15N] GIBBERELLA ZEAE CYANOVIRIN-N HOMOLOG-1, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-100% 15N] GzCVNH-2, 1.5 mM [U-100% 13C] GzCVNH-3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMGIBBERELLA ZEAE CYANOVIRIN-N HOMOLOG-1[U-100% 15N]1
1.5 mMGzCVNH-2[U-100% 15N]2
1.5 mMGzCVNH-3[U-100% 13C]2
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE6001
BRUKER AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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