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- PDB-5m2h: Crystal structure of vancomycin-Zn(II)-citrate complex -

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Basic information

Entry
Database: PDB / ID: 5m2h
TitleCrystal structure of vancomycin-Zn(II)-citrate complex
ComponentsVancomycin
KeywordsANTIBIOTIC / Vancomycin / zinc / glycopeptide
Function / homologyVancomycin / CITRIC ACID / :
Function and homology information
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.95 Å
AuthorsZarkan, A. / Macklyne, H.-R. / Chirgadze, D.Y. / Bond, A.D. / Hesketh, A.R. / Hong, H.-J.
CitationJournal: Sci Rep / Year: 2017
Title: Zn(II) mediates vancomycin polymerization and potentiates its antibiotic activity against resistant bacteria.
Authors: Zarkan, A. / Macklyne, H.R. / Chirgadze, D.Y. / Bond, A.D. / Hesketh, A.R. / Hong, H.J.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_molecule_features ...pdbx_entry_details / pdbx_molecule_features / pdbx_struct_special_symmetry / struct_ref
Item: _struct_ref.db_name / _struct_ref.pdbx_db_accession
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: diffrn_source / entity_poly / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vancomycin
B: Vancomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6798
Polymers2,3002
Non-polymers1,3796
Water1,33374
1
A: Vancomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9235
Polymers1,1501
Non-polymers7734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vancomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7563
Polymers1,1501
Non-polymers6062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.038, 57.481, 21.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

21B-202-

HOH

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Components

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Protein/peptide / Sugars , 2 types, 4 molecules AB

#1: Protein/peptide Vancomycin


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4.
Source: (natural) 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

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Non-polymers , 4 types, 78 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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.

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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: 62.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen citrate salt and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 0.95→37.31 Å / Num. obs: 19399 / % possible obs: 98.2 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.1
Reflection shellResolution: 0.95→1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 11.7 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 0.95→37.31 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.261 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.016 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11758 1939 10 %RANDOM
Rwork0.1049 ---
obs0.10616 17433 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 5.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 0.95→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms160 0 86 74 320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.02260
X-RAY DIFFRACTIONr_bond_other_d0.010.02181
X-RAY DIFFRACTIONr_angle_refined_deg2.7382.832341
X-RAY DIFFRACTIONr_angle_other_deg4.9253403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.75658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.787302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.751152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.220.238
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.02216
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0252
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5960.40354
X-RAY DIFFRACTIONr_mcbond_other0.5880.453
X-RAY DIFFRACTIONr_mcangle_it0.6130.58252
X-RAY DIFFRACTIONr_mcangle_other0.6080.58353
X-RAY DIFFRACTIONr_scbond_it0.9080.517206
X-RAY DIFFRACTIONr_scbond_other0.9110.516206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0380.758290
X-RAY DIFFRACTIONr_long_range_B_refined2.2476.389373
X-RAY DIFFRACTIONr_long_range_B_other1.3214.975325
X-RAY DIFFRACTIONr_rigid_bond_restr6.9373440
X-RAY DIFFRACTIONr_sphericity_free31.70659
X-RAY DIFFRACTIONr_sphericity_bonded5.6035491
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.113 119 -
Rwork0.098 1063 -
obs--81.63 %

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