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Basic information

Entry
Database: PDB / ID: 3run
TitleNew strategy to analyze structures of glycopeptide antibiotic-target complexes
Components
  • LYSOZYME
  • VANCOMYCIN
KeywordsHYDROLASE/ANTIBIOTIC / antibiotic / glycopeptide / native protein ligation / fusion / carboxymethylation of cysteine / vancomycin / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vancomycin / ISOPROPYL ALCOHOL / PHOSPHATE ION / : / Endolysin
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T4 (virus)
Streptomyces orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsEconomou, N.J. / Townsend, T.M. / 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 27, 2013Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_special_symmetry / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _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.pdbx_ptnr1_label_alt_id / _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
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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
B: VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,21911
Polymers20,1692
Non-polymers1,0519
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.440, 60.440, 96.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21B-206-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein LYSOZYME / / Endolysin / Lysis protein / Muramidase


Mass: 19018.799 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus) / Gene: E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00720, lysozyme
#2: Protein/peptide VANCOMYCIN / /


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 1 / 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) Streptomyces orientalis (bacteria) / References: NOR: NOR00681, Vancomycin
#3: Polysaccharide vancosamine-(1-2)-beta-D-glucopyranose /


Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 323.340 Da / Num. of mol.: 1
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 , 7 types, 324 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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 TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER. GROUP: 1 NAME: VANCOMYCIN CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 COMPONENT_2: SUGAR (2-MER) RESIDUES 8 AND 9 DESCRIPTION: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. 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.
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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M ammonium phosphate, 0.1M Tris 8.5, 35% MPD, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorDate: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→19.8 Å / Num. all: 77978 / Num. obs: 77081 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.48 % / Biso Wilson estimate: 18.614 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.4-1.440.7670.6522.0419858581651000.74587.7
1.44-1.480.5650.5332.925898561654640.59797.3
1.48-1.520.4250.4563.8230478549154910.504100
1.52-1.570.3350.3574.8129463528652860.394100
1.57-1.620.280.3045.6128566510851070.336100
1.62-1.670.2370.2566.5328005499149910.282100
1.67-1.740.1810.2097.9427119481248120.23100
1.74-1.810.1520.1749.3526186463346320.192100
1.81-1.890.1180.13711.5325186443544340.151100
1.89-1.980.0930.10913.9323855420042000.12100
1.98-2.090.0670.08517.6223103405240510.094100
2.09-2.210.0510.0720.7621687378937890.077100
2.21-2.370.0420.06123.2720628360236020.067100
2.37-2.560.0380.05724.4419098333333330.063100
2.56-2.80.0350.05127.3817592305330530.056100
2.8-3.130.0290.04630.4615992277527750.051100
3.13-3.610.0230.04134.7314074245224520.045100
3.61-4.430.0210.04137.411829206620660.045100
4.43-6.260.0230.04135.999135159315930.045100
6.260.0230.04237.3847668758500.04797.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.56 Å19.78 Å
Translation1.56 Å19.78 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: 2LZM

2lzm


Resolution: 1.4→19.784 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9234 / SU ML: 0.18 / σ(F): 1.43 / Phase error: 14.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 3879 5.03 %RANDOM
Rwork0.1475 ---
obs0.1491 77081 98.88 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.717 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 64.45 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.3277 Å2-0 Å20 Å2
2---0.3277 Å2-0 Å2
3---0.6554 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 67 316 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081541
X-RAY DIFFRACTIONf_angle_d1.3172099
X-RAY DIFFRACTIONf_dihedral_angle_d15.028599
X-RAY DIFFRACTIONf_chiral_restr0.069234
X-RAY DIFFRACTIONf_plane_restr0.007257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4001-1.45010.26843770.237660489
1.4501-1.50810.20083690.1834738999
1.5081-1.57680.19184070.16587359100
1.5768-1.65980.19544030.14477421100
1.6598-1.76380.17454210.13097366100
1.7638-1.89990.15763680.12037424100
1.8999-2.09090.17154030.13977383100
2.0909-2.3930.17093780.13747406100
2.393-3.01320.18043910.14527416100
3.0132-19.78560.1733620.1497434100

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