Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 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. Source: (gene. exp.) 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.: 45 / 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 TOUGHER 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: 1
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Sample preparation
Crystal
Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 %
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.918 Å / Relative weight: 1
Reflection
Resolution: 1→20 Å / Num. obs: 13896 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 16.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.8
Reflection shell
Resolution: 1→1.04 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.065 / % possible all: 54
Reflection
*PLUS
Num. measured all: 235187
Reflection shell
*PLUS
% possible obs: 54 %
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Processing
Software
Name
Classification
SHELXL
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Resolution: 1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: REFINEMENT WAS CARRIED OUT AGAINST F -SQUARED USING SHELXL-93. MOLECULAR GEOMETRY AND ATOMIC DISPLACEMENT PARAMETERS WERE RESTRAINED THROUGHOUT. INDEPENDENT VANCOMYCIN MONOMERS WERE ...Details: REFINEMENT WAS CARRIED OUT AGAINST F -SQUARED USING SHELXL-93. MOLECULAR GEOMETRY AND ATOMIC DISPLACEMENT PARAMETERS WERE RESTRAINED THROUGHOUT. INDEPENDENT VANCOMYCIN MONOMERS WERE RESTRAINED TO HAVE SIMILAR 1-2 AND 1-3 DISTANCES; RESTRAINTS WERE ALSO IMPOSED TO LIMIT DEVIATIONS FROM PLANARITY IN RINGS AND SP2 SYSTEMS. ALONG-BOND COMPONENTS OF ANISOTROPIC DISPLACEMENT PARAMETERS WERE SUBJECTED TO RESTRAINTS. SOLVENT WATER ATOMS WERE RESTRAINED TO BE APPROXIMATELY ISOTROPIC AND WERE MADE SUBJECT TO ANTI-BUMPING RESTRAINTS. CONJUGATE GRADIENT REFINEMENT WAS USED THROUGHOUT, EXCEPT AT THE LAST STAGES, WHEN BLOCKED LEAST SQUARES WAS USED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.142
934
-
RANDOM
obs
0.114
-
97 %
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all
-
14301
-
-
Refinement step
Cycle: LAST / Resolution: 1→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
160
0
51
45
256
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
s_bond_d
0.019
X-RAY DIFFRACTION
s_angle_d
X-RAY DIFFRACTION
s_similar_dist
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
X-RAY DIFFRACTION
s_similar_adp_cmpnt
X-RAY DIFFRACTION
s_approx_iso_adps
+
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