1IIY

Solution NMR Structure of Complex of 1:2 Cyanovirin-N:Man-Alpha1,2-Man-Alpha Restrained Regularized Mean Coordinates


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
1TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH 6.4300
2CBCANH 6.4300
3HCCH-COSY 6.4300
4HCCH-TOCSY 6.4300
515N-SEPARATED HOHAHA 6.4300
6QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS 6.4300
7DIPOLAR COUPLINGS OBTAINED BY TAKING THE DIFFERENCE IN THE J SPLITTINGS IN ISOTROPIC MEDIUM AND IN A LIQUID CRYSTALLINE MEDIUM (5% C12E5, R=0.96) (RUCKERT & OTTING (2000) J.AM.CHEM.SOC. 122, 7793-7797) MEASURED IN 2D IPAP (15N, 1H)-HSQC EXPERIMENTS (OTTIGER ET AL (1998) J.AM.CHEM.SOC. 131, 373-378) 6.4300
8INTERMOLECULAR DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED/13C-SEPARATED AND 15N-SEPARATED NOE EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA 6.4300
9INTRA-DISACCHARIDE AND INTER-MANNOPYRANOSE DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED NOE AND HOHAHA EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA. 6.4300
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDMX500500
2BrukerDMX600600
NMR Refinement
MethodDetailsSoftware
CONJOINED RIGID BODY/TORSION ANGLE DYNAMICSTHE STRUCTURE OF THE 1:1 COMPLEX IN WHICH DISACCHARIDE IS BOUND EXCLUSIVELY THROUGH THE HIGH AFFINITY SITE WAS CALCULATED USING CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016; WANG ET AL. (2001) EMBO. J., 19, 5635-5649 & REFS THEREIN) IN WHICH THE PROTEIN BACKBONE AND NON-INTERFACIAL SIDE CHAINS ARE HELD FIXED AND THE DISACCHARIDE AND INTERFACIAL SIDE CHAINS ARE FREE TO TRANSLATE AND ROTATE SUBJECT TO EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS. THE STRUCTURE OF THE DISACCHARIDE BOUND THROUGH THE LOW AFFINITY SITE IS A MODEL CALCULATED FROM A COMBINATION OF EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS, AND ADDITIONAL RESTRAINTS INTRODUCED ON THE BASIS OF SYMMETRY PRESENT BETWEEN THE TWO DOMAINS (HIGH AND LOW AFFINITY). THE NMR COORDINATES FOR MONOMERIC CVN (PDB ACC. 2EZM) WERE USED FOR THE STARTING COORDINATES WITH 2 EQ. OF MAN-ALPHA-1,2-MAN-ALPHA POSITIONED WITHIN 10 A OF THE PREVIOUSLY MAPPED CARBOHYDRATE BINDING SITES (BEWLEY & OTERO-QUINTERO (2001) J.AM.CHEM.SOC. IN PRESS).X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number50
Conformers Submitted Total Number1
Additional NMR Experimental Information
DetailsThis structure is the restrained regularized mean structure. IN THIS ENTRY THE ELEVENTH COLUMN OF THE COORDINATES (with "atom" as the first column) REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE 50 INDIVIDUAL SIMULATED ANNEALING STRUCTURES HAVING ZERO DISTANCE VIOLATIONS GREATER THAN 0.2 A AND ZERO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEG. THE AVERAGE STRUCTURE WAS GENERATED BY BEST FITTING TO THE BACKBONE OF RESIDUES 1-101. NOTE THE OCCUPANCY FIELD in the tenth column has no meaning. AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND DISACCHARIDE OF THE HIGH AFFINITY SITE=0.36. AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND DISACCHARIDE OF THE LOW AFFINITY SITE=0.58. RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, NOE, CDIH 6.389414E-03 0.717363 0.693234 8.897236E-03 9.181435E-02.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementX-PLORNIHBRUNGER