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- PDB-1fvm: Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA -

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Basic information

Entry
Database: PDB / ID: 1fvm
TitleComplex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA
Components
  • DI-ACETYL-LYS-D-ALA-D-ALA
  • VANCOMYCIN
KeywordsPEPTIDE/ANTIBIOTIC / PEPTIDE-ANTIBIOTIC COMPLEX / GLYCOPEPTIDE / ANTIBIOTIC / VANCOMYCIN / CELL WALL PRECURSOR / STRUCTURAL PROTEIN-ANTIBIOTIC COMPLEX
Function / homologyVancomycin / :
Function and homology information
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNitanai, Y. / Kakoi, K. / Aoki, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of the Complexes between Vancomycin and Cell-Wall Precursor Analogs.
Authors: Nitanai, Y. / Kikuchi, T. / Kakoi, K. / Hanamaki, S. / Fujisawa, I. / Aoki, K.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2000Provider: 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 / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / 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 / 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 / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VANCOMYCIN
B: VANCOMYCIN
C: VANCOMYCIN
D: VANCOMYCIN
E: VANCOMYCIN
F: VANCOMYCIN
G: DI-ACETYL-LYS-D-ALA-D-ALA
H: DI-ACETYL-LYS-D-ALA-D-ALA
I: DI-ACETYL-LYS-D-ALA-D-ALA
J: DI-ACETYL-LYS-D-ALA-D-ALA
K: DI-ACETYL-LYS-D-ALA-D-ALA
L: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,07418
Polymers9,13412
Non-polymers1,9406
Water2,018112
1
A: VANCOMYCIN
G: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8463
Polymers1,5222
Non-polymers3231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-2.9 kcal/mol
Surface area1540 Å2
MethodPISA
2
B: VANCOMYCIN
H: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8463
Polymers1,5222
Non-polymers3231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-3.6 kcal/mol
Surface area1480 Å2
MethodPISA
3
C: VANCOMYCIN
I: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8463
Polymers1,5222
Non-polymers3231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-2.6 kcal/mol
Surface area1540 Å2
MethodPISA
4
D: VANCOMYCIN
J: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8463
Polymers1,5222
Non-polymers3231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-2.7 kcal/mol
Surface area1630 Å2
MethodPISA
5
E: VANCOMYCIN
K: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8463
Polymers1,5222
Non-polymers3231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-3.2 kcal/mol
Surface area1430 Å2
MethodPISA
6
F: VANCOMYCIN
L: DI-ACETYL-LYS-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8463
Polymers1,5222
Non-polymers3231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-2.7 kcal/mol
Surface area1640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.637, 36.425, 65.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
VANCOMYCIN / /


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: SEQUENCE OCCURS IN NOCARDIA ORIENTALIS / Source: (synth.) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, Vancomycin
#2: Protein/peptide
DI-ACETYL-LYS-D-ALA-D-ALA


Mass: 372.417 Da / Num. of mol.: 6 / Source method: obtained synthetically
#3: Polysaccharide
vancosamine-(1-2)-beta-D-glucopyranose /


Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 323.340 Da / Num. of mol.: 6
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.95 Å3/Da / Density % sol: 37.1 %
Crystal growpH: 8.5
Details: CRYSTALS WERE PREPARED AT 293K FROM A SOLUTION CONTAINING 6.6 MM VANCOMYCIN, 6.6 MM DI- ACETYL-LYS -D-ALA-D-ALA, 3.3 % (V/V) ETHANOL, AND 0.66 M TRIS BUFFER PH 8.5, BY EQUILIBRATING THE ...Details: CRYSTALS WERE PREPARED AT 293K FROM A SOLUTION CONTAINING 6.6 MM VANCOMYCIN, 6.6 MM DI- ACETYL-LYS -D-ALA-D-ALA, 3.3 % (V/V) ETHANOL, AND 0.66 M TRIS BUFFER PH 8.5, BY EQUILIBRATING THE SOLUTION AGAINST A RESERVOIR SOLUTION CONTAINING 10 % (V/V) ETHANOL AND 0.2 M TRIS BUFFER PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC QUAMTUM 4R / Detector: CCD / Date: Jun 24, 2000 / Details: MIRRORS
RadiationMonochromator: FOCUSSING SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25.5 Å / Num. obs: 8400 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.043 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 8.5 / Rsym value: 0.066 / % possible all: 99.9

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AA5

1aa5


Resolution: 1.8→5 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.144 --
obs0.144 7864 99 %
Displacement parametersBiso mean: 8.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 0 126 112 874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.05
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d0.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.352
X-RAY DIFFRACTIONx_scangle_it1.972.5
LS refinement shellResolution: 1.8→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.148 382 -
obs--95.7 %
Xplor fileSerial no: 1 / Param file: PARAM19X.SOL / Topol file: TOPH19.SOL

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