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Basic information

Entry
Database: PDB / ID: 3rum
TitleNew strategy to analyze structures of glycopeptide antibiotic-target complexes
Components
  • Maltose-binding periplasmic protein
  • Ristocetin
KeywordsSUGAR BINDING PROTEIN/ANTIBIOTIC / antibiotic / glycopeptide / native protein ligation / fusion / carboxymethylation of cysteine / ristocetin / SUGAR BINDING PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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
alpha-maltose / ISOPROPYL ALCOHOL / alpha-D-mannopyranose / 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Amycolatopsis lurida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.851 Å
AuthorsEconomou, N.J. / Weeks, S.D. / Grasty, K.C. / Nahoum, V. / Loll, P.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: A carrier protein strategy yields the structure of dalbavancin.
Authors: Economou, N.J. / Nahoum, V. / Weeks, S.D. / Grasty, K.C. / Zentner, I.J. / Townsend, T.M. / Bhuiya, M.W. / Cocklin, S. / Loll, P.J.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Derived calculations / Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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 2.2Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
B: Ristocetin
C: Ristocetin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,51017
Polymers43,7073
Non-polymers2,80314
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.833, 75.005, 90.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 41342.777 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Protein/peptide Ristocetin


Mass: 1182.147 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amycolatopsis lurida (bacteria)

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Sugars , 4 types, 7 molecules

#3: Polysaccharide alpha-D-arabinofuranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-6)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 620.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DArafa1-2DManpa1-2[LRhapa1-6]DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5][a1122h-1a_1-5][a122h-1a_1-4][a2211m-1a_1-5]/1-2-3-4/a2-b1_a6-d1_b2-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Araf]{}}[(6+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-RST / 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose / RISTOSAMINE / 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexose / 3-amino-2,3,6-trideoxy-L-ribo-hexose / 3-amino-2,3,6-trideoxy-ribo-hexose


Type: L-saccharide, alpha linking / Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#8: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
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 , 3 types, 390 molecules

#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRISTOCETIN IS A TETRACYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-L- ...RISTOCETIN IS A TETRACYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-L-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A TETRASACCHARIDE MADE OF D-GLUCOSE L-RHAMNOSE, D-MANNOSE, AND D-ARABINOFURANOSE, AND MONSACCHARIDES RISTOSAMINE AND D-MANNOSE. HERE, RISTOCETIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE SIX LIGANDS (HET) BGC, RAM, MAN, BXY, RST, AND MAN. GROUP: 1 NAME: RISTOCETIN CHAIN: B, C COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 COMPONENT_2: SUGAR (4-MER) 8, 9, 10, 11 COMPONENT_3: SUGAR (RISTOSAMINE) 12 COMPONENT_4: SUGAR (ALPHA-D-MANNOSE) 13 DESCRIPTION: RISTOCETIN IS A TETRACYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A TETRASACCHARIDE (RESIDUES 8, 9, 10, and 11) ON RESIDUE 4, A MONOSACCHARIDE ON RESIDUE 6 (RESIDUE 12), AND A MONOSACCHARIDE ON RESIDUE 7 (RESIDUE 13).
Sequence detailsTHE AUTHORS STATE THAT THESE RESIDUES ARE LIGATED NON-RECOMBINANTLY WITH NATIVE PROTEIN LIGATION ...THE AUTHORS STATE THAT THESE RESIDUES ARE LIGATED NON-RECOMBINANTLY WITH NATIVE PROTEIN LIGATION AFTER PROTEIN EXPRESSION AND PURIFICATION.

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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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 5% isopropanol, 2M ammonium sulfate, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537 Å
DetectorDate: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→19.42 Å / Num. all: 34368 / Num. obs: 33176 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 4.06 %

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.92 Å19.42 Å
Translation1.92 Å19.42 Å

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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
Starting model: 1ANF

1anf


Resolution: 1.851→19.416 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 1.99 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 1702 5.13 %
Rwork0.1762 --
obs0.1785 33176 96.63 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.06 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.112 Å2-0 Å20 Å2
2---4.0171 Å2-0 Å2
3---7.1291 Å2
Refinement stepCycle: LAST / Resolution: 1.851→19.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 177 383 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073357
X-RAY DIFFRACTIONf_angle_d1.234600
X-RAY DIFFRACTIONf_dihedral_angle_d12.3051267
X-RAY DIFFRACTIONf_chiral_restr0.075519
X-RAY DIFFRACTIONf_plane_restr0.006567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8509-1.9170.28541460.24862591X-RAY DIFFRACTION81
1.917-1.99370.31441490.22172995X-RAY DIFFRACTION92
1.9937-2.08430.24481710.20213119X-RAY DIFFRACTION97
2.0843-2.19410.22041850.18173181X-RAY DIFFRACTION99
2.1941-2.33140.24661900.1813182X-RAY DIFFRACTION99
2.3314-2.5110.23471880.17343221X-RAY DIFFRACTION100
2.511-2.76310.21791500.18083265X-RAY DIFFRACTION100
2.7631-3.16140.21121530.18123266X-RAY DIFFRACTION100
3.1614-3.97740.21331730.15553285X-RAY DIFFRACTION99
3.9774-19.41720.18311970.16093364X-RAY DIFFRACTION98

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