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- PDB-1ghg: CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON -

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Basic information

Entry
Database: PDB / ID: 1ghg
TitleCRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON
ComponentsVANCOMYCIN AGLYCON
KeywordsANTIBIOTIC / GLYCOPEPTIDE / AGLYCON / VANCOMYCIN
Function / homologynor:nor00681: / VANCOMYCIN AGLYCON
Function and homology information
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.98 Å
AuthorsKaplan, J. / Korty, B.D. / Axelsen, P.H. / Loll, P.J.
CitationJournal: J.Med.Chem. / Year: 2001
Title: The Role of Sugar Residues in Molecular Recognition by Vancomycin
Authors: Kaplan, J. / Korty, B.D. / Axelsen, P.H. / Loll, P.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2001Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VANCOMYCIN AGLYCON
B: VANCOMYCIN AGLYCON
C: VANCOMYCIN AGLYCON
D: VANCOMYCIN AGLYCON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,99610
Polymers4,6004
Non-polymers3966
Water1,20767
1
A: VANCOMYCIN AGLYCON
B: VANCOMYCIN AGLYCON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4204
Polymers2,3002
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: VANCOMYCIN AGLYCON
D: VANCOMYCIN AGLYCON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5766
Polymers2,3002
Non-polymers2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)29.480, 29.480, 74.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-2003-

HOH

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Components

#1: Protein/peptide
VANCOMYCIN AGLYCON


Type: Oligopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: VANCOMYCIN AGLYCON IS THE NONSUGAR COMPONENT OF VANCOMYCIN, CONSISTING OF THE TRICYCLIC HEPTAPEPTIDE ONLY.
Source: (synth.) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, VANCOMYCIN AGLYCON
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVANCOMYCIN 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 AGLYCON IS REPRESENTED BY SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.87 %
Crystal growpH: 6.9
Details: 100 MM SODIUM CACODYLATE, 1.6 M SODIUM ACETATE, PH 6.9, VAPOR DIFFUSION/HANGING DROP, TEMPERATURE 277K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 %(v/v)DMSO1drop
31.5 Msodium acetate1reservoir
4100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 0.98→8 Å / Num. obs: 16377 / % possible obs: 87.2 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.8
Reflection shellResolution: 0.98→1.08 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.238 / % possible all: 66.7

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Processing

Software
NameClassification
SnBphasing
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 0.98→8 Å / σ(F): 4
Stereochemistry target values: THE FOUR COPIES OF THE MOLECULE IN THE ASYMMETRIC UNIT WERE RESTRAINED TO HAVE SIMLAR 1,2- AND 1,3-DISTANCES. SP2 CENTERS AND RINGS WERE RESTRAINED TO PLANARITY.
Details: CONJUGATE GRADIENT FOR MOST OF REFINEMENT, FOLLOWED BY BLOCKED LEAST SQUARES
RfactorNum. reflection% reflection
Rfree0.15 1422 8.3 %
All0.15 17071 -
Obs0.15 -90.9 %
Refinement stepCycle: LAST / Resolution: 0.98→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms320 0 24 67 411
Software
*PLUS
Name: SHELXL / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 8.3 % / Rfactor all: 0.15 / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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