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- PDB-2ezm: SOLUTION NMR STRUCTURE OF CYANOVIRIN-N, RESTRAINED REGULARIZED ME... -

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Basic information

Entry
Database: PDB / ID: 2ezm
TitleSOLUTION NMR STRUCTURE OF CYANOVIRIN-N, RESTRAINED REGULARIZED MEAN COORDINATES
ComponentsCYANOVIRIN-N
KeywordsHIV-INACTIVATING PROTEIN
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
AuthorsBewley, C.A. / Gronenborn, A.M. / Clore, G.M.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Solution structure of cyanovirin-N, a potent HIV-inactivating protein.
Authors: Bewley, C.A. / Gustafson, K.R. / Boyd, M.R. / Covell, D.G. / Bax, A. / Clore, G.M. / Gronenborn, A.M.
History
DepositionMay 6, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)11,0221
Polymers11,0221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein CYANOVIRIN-N /


Mass: 11022.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc ellipsosporum (bacteria) / References: UniProt: P81180

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
121CBCANH
131HNCO
141C(CO)NH
151H(CCO)NH
161(H)CCH-COSY
171(H)CCH-TOCSY
181HNHA
19115N-SEPARATED HOHAHA; QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; 3D 15N-SEPARATED NOE
11013D 13C-SEPARATED NOE AND ROE
11114D 15N/13C-SEPARATED NOE
11214D 13C/13C-SEPARATED NOE EXPERIMENTS; 3D HCA(CO)N FOR THREE-BOND AMINIDE DEUTERIUM ISOTOPE SHIFTS; VARIOUS COUPLED 2D AND 3D SPECTRA TO MEASURE THE N-H
1131CA-H
1141C-H CA-C'
1151N-C'
1161HN-C' DIPOLAR COUPLINGS OBTAINED BY TAKING THE DIFFERENCE IN THE J SPLITTINGS IN ISOTROPIC MEDIUM
1171IN A LIQUID CRYSTALLINE MEDIUM (4% 3:1 DMPC:DHPC).
NMR detailsText: THE 3D STRUCTURE OF CYANOVIRIN SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 2597 EXPERIMENTAL NMR RESTRAINTS: 419 SEQUENTIAL (|I- J|=1), 170 MEDIUM RANGE (1 < |I-J| 5) ...Text: THE 3D STRUCTURE OF CYANOVIRIN SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 2597 EXPERIMENTAL NMR RESTRAINTS: 419 SEQUENTIAL (|I- J|=1), 170 MEDIUM RANGE (1 < |I-J| <=5) AND 554 LONG RANGE (|I-J| >5) INTERRESIDUES AND 19 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 109 DISTANCE RESTRAINTS FOR 55 H-BONDS; 339 TORSION ANGLE RESTRAINTS (100 PHI, 98 PSI, 76 CHI1, 48 CHI2, 15 CHI3, 2 CHI4); 82 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 157 (82 CALPHA AND 75 CBETA) 13C SHIFT RESTRAINTS; 362 1H SHIFT RESTRAINTS; AND 386 DIPOLAR COUPLING RESTRAINTS (82 N-H, 76 C-H, 43 CA-C', 65 N-C' 62 HNC', 58 SIDE-CHAIN C-H). THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM CNS (BRUNGER ET AL. ACTA CRYST SERIES D IN PRESS) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96), 1H CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 107, 293-297; KUSZEWSKI ET AL. (1996) J. MAGN. RESON. SERIES B 112, 79-81), AND DIPOLAR COUPLING (CLORE ET AL. (1998) J. MAGN. RESON. 131, 159-162) RESTRAINTS, AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI. 5, 1067-1080; KUSZEWSKI ET AL. (1997) J. MAGN. RESON 125, 171-177).

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DMX750BrukerDMX7507503

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
NMR software
NameDeveloperClassification
CNSBRUNGER, ADAMS, CLORE, DELANO, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: AVE.RMS DIFF. TO MEAN FOR ALL NON-H-ATOMS (RESIDUES 1:101)= 0.433636 AVE.RMS DIFF. TO MEAN FOR BACKBONE ATOMS (N, CA, C', O) (RESIDUES 1:101)= 0.139826 RMS DEVIATIONS FOR BONDS, ANGLES, ...Details: AVE.RMS DIFF. TO MEAN FOR ALL NON-H-ATOMS (RESIDUES 1:101)= 0.433636 AVE.RMS DIFF. TO MEAN FOR BACKBONE ATOMS (N, CA, C', O) (RESIDUES 1:101)= 0.139826 RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, CDIH, NOE, COUP 5.067337E-03, 0.712983, 0.667194, 0.157308, 1.428009E-02, 0.608909 C13CA AND CB SHIFTS RMS : 0.852581, 1.15742 JCOUP STATS: NON-GLY RESIDUES GLY RMS-D: 0.608909 1.46813 BACKBONE DIPOLAR COUPLINGS NH CH CACO NCO HNCO RMS : 0.466712 1.15058 1.29414 0.572019 1.2653 SIDECHAIN DIPOLAR COUPLINGS CH CH3S CH3D ARO RMS DIPO_SIDE: 1.6875 0.796796 0.531907 0.160016 RMS FOR 1H SHIFTS: ALL ALPHA ALPHA_GLY METHYL(S) METHYL(D) OTHER(S) OTHER(D) RMS PROT: 0.263524 0.243015 0.23853 0.115892 0.148148 0.267304 0.300122 IN THE RESTRAINED REGULARIZED MEAN COORDINATES (2EZM) THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES (2EZN) HAS NO MEANING. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 1-101. NOTE THE OCCUPANCY FIELD HAS NO MEANING.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers submitted total number: 1

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