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- PDB-8g82: Vancomycin bound to D-Ala-D-Ser -

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Basic information

Entry
Database: PDB / ID: 8g82
TitleVancomycin bound to D-Ala-D-Ser
Components
  • D-Ala-D-Ser
  • Vancomycin
KeywordsANTIBIOTIC / Antibiotic resistance
Function / homologybeta-D-glucopyranose / BORIC ACID / TRIETHYLENE GLYCOL / vancosamine / polypeptide(D)
Function and homology information
Biological speciesAmycolatopsis orientalis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLoll, P.J. / Park, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI148679 United States
CitationJournal: Iucrj / Year: 2024
Title: Crystal structure of vancomycin bound to the resistance determinant D-alanine-D-serine.
Authors: Park, J.H. / Reviello, R.E. / Loll, P.J.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vancomycin
B: Vancomycin
C: Vancomycin
D: Vancomycin
E: Vancomycin
F: Vancomycin
G: Vancomycin
H: Vancomycin
I: Vancomycin
J: Vancomycin
K: D-Ala-D-Ser
L: D-Ala-D-Ser
M: D-Ala-D-Ser
N: D-Ala-D-Ser
O: D-Ala-D-Ser
P: D-Ala-D-Ser
Q: D-Ala-D-Ser
R: D-Ala-D-Ser
S: D-Ala-D-Ser
T: D-Ala-D-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,43940
Polymers13,52220
Non-polymers3,91820
Water4,648258
1
A: Vancomycin
B: Vancomycin
K: D-Ala-D-Ser
L: D-Ala-D-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5017
Polymers2,7044
Non-polymers7973
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vancomycin
D: Vancomycin
M: D-Ala-D-Ser
N: D-Ala-D-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4137
Polymers2,7044
Non-polymers7093
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Vancomycin
F: Vancomycin
O: D-Ala-D-Ser
P: D-Ala-D-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4137
Polymers2,7044
Non-polymers7093
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Vancomycin
H: Vancomycin
Q: D-Ala-D-Ser
R: D-Ala-D-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,62111
Polymers2,7044
Non-polymers9177
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Vancomycin
J: Vancomycin
S: D-Ala-D-Ser
T: D-Ala-D-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4918
Polymers2,7044
Non-polymers7874
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.490, 71.150, 82.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein/peptide / Polypeptide(D) , 2 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein/peptide
Vancomycin


Mass: 1149.977 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Amycolatopsis orientalis (bacteria)
#2: Polypeptide(D)
D-Ala-D-Ser


Mass: 202.209 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 12 molecules

#3: Polysaccharide
vancosamine-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 323.340 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-RER / vancosamine / (1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose


Type: L-saccharide, alpha linking / Mass: 161.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H15NO3 / Comment: antibiotic*YM

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Non-polymers , 4 types, 266 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: BH3O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

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 IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6 / Details: 25% PEG 1500, 100 mM MIB buffer pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92133605558445 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92133605558445 Å / Relative weight: 1
ReflectionResolution: 1.2→26.54 Å / Num. obs: 53037 / % possible obs: 93 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.59 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.49
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 3.06 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.72 / % possible all: 59.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→26.53 Å / SU ML: 0.099 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.109
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2000 3.77 %random
Rwork0.153 ---
obs0.154 53028 93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.28 Å2
Refinement stepCycle: LAST / Resolution: 1.2→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 188 258 1456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121295
X-RAY DIFFRACTIONf_angle_d1.7571802
X-RAY DIFFRACTIONf_dihedral_angle_d54.602491
X-RAY DIFFRACTIONf_chiral_restr0.089222
X-RAY DIFFRACTIONf_plane_restr0.02169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.2923910.23252323X-RAY DIFFRACTION60
1.23-1.260.21541060.20062703X-RAY DIFFRACTION70
1.26-1.30.20651280.18273252X-RAY DIFFRACTION84
1.3-1.340.21411460.16173747X-RAY DIFFRACTION97
1.34-1.390.19241500.14823812X-RAY DIFFRACTION99
1.39-1.450.16021520.13223876X-RAY DIFFRACTION100
1.45-1.510.16811500.13223845X-RAY DIFFRACTION99
1.51-1.590.18581520.12353866X-RAY DIFFRACTION99
1.59-1.690.15371530.12673897X-RAY DIFFRACTION99
1.69-1.820.19371520.13573872X-RAY DIFFRACTION99
1.82-2.010.15361520.13553912X-RAY DIFFRACTION100
2.01-2.30.15191540.14273925X-RAY DIFFRACTION99
2.3-2.890.18551560.16363943X-RAY DIFFRACTION99
2.89-26.530.16031580.16614055X-RAY DIFFRACTION97

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