Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Solution NMR Structure of Complex of 1:2 Cyanovirin-N:Man-Alpha1,2-Man-Alpha Restrained Regularized Mean Coordinates
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
6.4
300
2
CBCANH
6.4
300
3
HCCH-COSY
6.4
300
4
HCCH-TOCSY
6.4
300
5
15N-SEPARATED HOHAHA
6.4
300
6
QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
6.4
300
7
DIPOLAR 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)
6.4
300
8
INTERMOLECULAR 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
6.4
300
9
INTRA-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.
6.4
300
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX500
500
2
Bruker
DMX600
600
NMR Refinement
Method
Details
Software
CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS
THE 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 Number
50
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
This 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.