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- PDB-3vfj: The structure of monodechloro-teicoplanin in complex with its lig... -

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Basic information

Entry
Database: PDB / ID: 3vfj
TitleThe structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a ligand carrier
Components
  • Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala
  • MonodeChloro- Teicoplanin A2-2
KeywordsSUGAR BINDING PROTEIN/ANTIBIOTIC / teicoplanin / acetylation of cyteine with iodoacetate modification / SUGAR BINDING PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MonodeChloro- Teicoplanin A2-2 / ACETATE ION / CACODYLATE ION / 2-amino-2-deoxy-beta-D-glucopyranose / alpha-D-mannopyranose / 8-METHYLNONANOIC ACID / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Actinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsEconomou, N.J. / Weeks, S.D. / Grasty, K.C. / Loll, P.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach.
Authors: Economou, N.J. / Zentner, I.J. / Lazo, E. / Jakoncic, J. / Stojanoff, V. / Weeks, S.D. / Grasty, K.C. / Cocklin, S. / Loll, P.J.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Structure summary
Revision 1.2Mar 13, 2013Group: Structure summary
Revision 1.3Mar 27, 2013Group: Derived calculations
Revision 1.4Apr 3, 2013Group: Derived calculations
Revision 1.5Jun 19, 2013Group: Database references
Revision 1.6Dec 10, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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 / _struct_ref_seq_dif.details
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: Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala
G: MonodeChloro- Teicoplanin A2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,18318
Polymers42,5152
Non-polymers1,66816
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-154 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.320, 123.610, 156.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AG

#1: Protein Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala / MBP / MMBP / Maltodextrin-binding protein


Mass: 41342.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: four C-terminal amino acids added non-recombinantly with native chemical ligation
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Protein/peptide MonodeChloro- Teicoplanin A2-2


Type: Glycopeptide / Class: Antibiotic / Mass: 1172.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinoplanes teichomyceticus (bacteria) / References: MonodeChloro- Teicoplanin A2-2

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Sugars , 3 types, 3 molecules

#6: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / 2-AMINO-2-DEOXY-D-GLUCOSE


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5 / References: MonodeChloro- Teicoplanin A2-2
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / References: MonodeChloro- Teicoplanin A2-2
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking, Glycopeptide / Class: Antibiotic / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / References: MonodeChloro- Teicoplanin A2-2
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 168 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical ChemComp-T55 / 8-METHYLNONANOIC ACID


Type: Glycopeptide / Class: Antibiotic / Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2 / References: MonodeChloro- Teicoplanin A2-2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAUTHORS STATED THE FOLLOWING: THE STARTING MATERIAL HAD TEICOPLANIN A2-2 THAT CONTAINED TWO ...AUTHORS STATED THE FOLLOWING: THE STARTING MATERIAL HAD TEICOPLANIN A2-2 THAT CONTAINED TWO CHLORINE ATOMS. THE ACTUAL CRYSTALS CONTAINED BOTH CHLORINE ATOMS BEFORE THEY WERE EXPOSED TO X-RAYS. ONE CHLORINE WAS REMOVED FROM TEICOPLANIN BY X-IRRADIATION DAMAGE EARLY IN THE DIFFRACTION EXPERIMENT TEICOPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE FURTHER GLYCOSYLATED BY THREE MONO SACCHARIDES: MANNOSE, N-ACETYLGLUCOSAMINE AND BETA-D-GLUCOSAMINE AND ONLY DIFFER BY THE SIDE CHAIN ATTACHED TO THE LATTER. TEICOPLANIN A2-2 HAS 8-METHYLNONANOIC ACID ATTACHED TO GLUCOSAMINE. HERE, TEICOPLANIN A2-2 WAS UNDER RADIATION DAMAGE, WHICH CAUSES THE LOSS OF ONE CHLORINE ATOM.
Sequence detailsC-TERMINAL FUSED BY LINKER AND MODIFIED CYS-LYS-D-ALA-D-ALA

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M zinc acetate, 0.1 M sodium cacodylate 6.5, 16% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2009
RadiationMonochromator: Si(111)side bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→39.89 Å / Num. obs: 47482 / % possible obs: 100 % / Observed criterion σ(I): -3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→39.89 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.24 / σ(F): 1.39 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 2385 5.02 %
Rwork0.188 --
obs0.1901 47469 99.94 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.663 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6758 Å2-0 Å20 Å2
2---4.739 Å2-0 Å2
3---4.0632 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 73 155 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063136
X-RAY DIFFRACTIONf_angle_d1.0454271
X-RAY DIFFRACTIONf_dihedral_angle_d11.9541153
X-RAY DIFFRACTIONf_chiral_restr0.067461
X-RAY DIFFRACTIONf_plane_restr0.008551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12330.30952540.25674520X-RAY DIFFRACTION100
2.1233-2.20830.27462480.22474471X-RAY DIFFRACTION100
2.2083-2.30880.25422460.21324476X-RAY DIFFRACTION100
2.3088-2.43050.26252100.19684527X-RAY DIFFRACTION100
2.4305-2.58270.22872210.20214538X-RAY DIFFRACTION100
2.5827-2.78210.28022660.19844493X-RAY DIFFRACTION100
2.7821-3.0620.2562210.19154528X-RAY DIFFRACTION100
3.062-3.50480.20852370.17434501X-RAY DIFFRACTION100
3.5048-4.41480.20552560.16224512X-RAY DIFFRACTION100
4.4148-39.90780.20082260.18314518X-RAY DIFFRACTION100

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