Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. Source: (synth.) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, Vancomycin
#2: Polysaccharide
vancosamine-(1-2)-beta-D-glucopyranose
Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 323.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. References: Vancomycin
Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound details
VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
Density Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal grow
pH: 4.6 Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF A 25 MG/ML VANCOMYCIN SOLUTION AND 2.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.6 (RESERVOIR BUFFER) AND THEN SUSPENDING THIS DROP OVER THE RESERVOIR. ...Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF A 25 MG/ML VANCOMYCIN SOLUTION AND 2.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.6 (RESERVOIR BUFFER) AND THEN SUSPENDING THIS DROP OVER THE RESERVOIR. CRYSTALS WERE GROWN AT 293 K., VAPOR DIFFUSION - HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.85 Å / Relative weight: 1
Reflection
Resolution: 0.89→10 Å / Num. obs: 17899 / % possible obs: 85.8 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rsym value: 0.076 / Net I/σ(I): 100
Reflection shell
Resolution: 0.89→0.95 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 31.5 / Rsym value: 0.143 / % possible all: 69.3
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 69.3 % / Rmerge(I) obs: 0.143
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Processing
Software
Name
Classification
SHELXL-93
modelbuilding
SHELXL-93
refinement
MADNES
datareduction
PROCOR
datareduction
XSCALE
datascaling
SHELXL-93
phasing
Refinement
Method to determine structure: DIRECT METHODS / Resolution: 0.89→4 Å / Num. parameters: 2553 / Num. restraintsaints: 3647 / σ(F): 0 Details: REFINEMENT WAS CARRIED OUT VS. F**2; SIMILAR 1,2 AND 1,3 DISTANCE RESTRAINTS WERE APPLIED TO THE TWO VANCOMYCIN MOLECULES. ALSO, RESTRAINTS WERE IMPOSED TO LIMIT DEVIATIONS OF RINGS AND ...Details: REFINEMENT WAS CARRIED OUT VS. F**2; SIMILAR 1,2 AND 1,3 DISTANCE RESTRAINTS WERE APPLIED TO THE TWO VANCOMYCIN MOLECULES. ALSO, RESTRAINTS WERE IMPOSED TO LIMIT DEVIATIONS OF RINGS AND PEPTIDE BONDS FROM PLANARITY AND DIFFERENCES IN ALONG-BOND COMPONENTS OF ADPS. ADPS FOR SOLVENT WERE RESTRAINED TO BE APPROXIMATELY ISOTROPIC, AND ANTIBUMPING RESTRAINTS WERE USED TO PREVENT SOLVENT WATER MOLECULES FROM VIOLATING MINIMUM CONTACT DISTANCES. CONJUGATE GRADIENT LEAST SQUARES WAS USED FOR MOST OF THE REFINEMENT, WITH BLOCKED LEAST SQUARES AT THE END.
Rfactor
Num. reflection
% reflection
all
0.124
17899
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obs
0.124
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80 %
Refine analyze
Num. disordered residues: 3 / Occupancy sum hydrogen: 158 / Occupancy sum non hydrogen: 255.4
Refinement step
Cycle: LAST / Resolution: 0.89→4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
160
0
50
55
265
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
s_bond_d
X-RAY DIFFRACTION
s_angle_d
X-RAY DIFFRACTION
s_similar_dist
0.019
X-RAY DIFFRACTION
s_from_restr_planes
X-RAY DIFFRACTION
s_zero_chiral_vol
X-RAY DIFFRACTION
s_non_zero_chiral_vol
X-RAY DIFFRACTION
s_anti_bump_dis_restr
X-RAY DIFFRACTION
s_rigid_bond_adp_cmpnt
0.008
X-RAY DIFFRACTION
s_similar_adp_cmpnt
0.011
X-RAY DIFFRACTION
s_approx_iso_adps
0.025
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