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- PDB-1sho: CRYSTAL STRUCTURE OF VANCOMYCIN AT ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1sho
TitleCRYSTAL STRUCTURE OF VANCOMYCIN AT ATOMIC RESOLUTION
ComponentsVANCOMYCIN
KeywordsANTIBIOTIC / GLYCOPEPTIDE
Function / homologyVancomycin / ACETATE ION / :
Function and homology information
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.09 Å
AuthorsSheldrick, G.M.
CitationJournal: Structure / Year: 1996
Title: Crystal Structure of Vancomycin.
Authors: Schafer, M. / Schneider, T.R. / Sheldrick, G.M.
History
DepositionJul 23, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / entity_poly / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VANCOMYCIN
B: VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0777
Polymers2,3002
Non-polymers7775
Water1,946108
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5.2 kcal/mol
Surface area1650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.480, 28.480, 65.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2035-

HOH

21B-2016-

HOH

31B-2017-

HOH

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Components

#1: Protein/peptide VANCOMYCIN / /


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
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
[][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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 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

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

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growpH: 5.8 / Details: PH 5.8
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
25 mMHEPES1drop
35 mMsodium acetate1drop
41 Msodium chloride1drop
510 mMsodium acetate1reservoir
62 Msodium chloride1reservoir

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.862
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 29, 1995 / Details: BENT CRYSTAL MONOCHROMATOR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.862 Å / Relative weight: 1
ReflectionResolution: 1.09→70 Å / Num. obs: 11867 / % possible obs: 99.3 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 27
Reflection shellResolution: 1.09→1.17 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 19.7 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELX-96model building
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELX-96phasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.09→70 Å / Num. parameters: 2867 / Num. restraintsaints: 3022
StereochEM target val spec case: ENGH AND HUBER RESTRAINT DISTANCES FOR ACETATE AND FOR THE TWO DISORDERED SUGARS
RfactorNum. reflection% reflection
obs0.105 -99.3 %
all-11867 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 155 / Occupancy sum non hydrogen: 314.5
Refinement stepCycle: LAST / Resolution: 1.09→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms160 0 48 108 316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.024
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.022
X-RAY DIFFRACTIONs_from_restr_planes0.057
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.041
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.017
X-RAY DIFFRACTIONs_approx_iso_adps0.104
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / Rfactor all: 0.1054 / Rfactor obs: 0.1036
Solvent computation
*PLUS
Displacement parameters
*PLUS

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