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- PDB-4pjz: CRYSTAL STRUCTURE OF T4 LYSOZYME-GSS-PEPTIDE IN COMPLEX WITH TEIC... -

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Basic information

Entry
Database: PDB / ID: 4pjz
TitleCRYSTAL STRUCTURE OF T4 LYSOZYME-GSS-PEPTIDE IN COMPLEX WITH TEICOPLANIN-A2-2
Components
  • Lysozyme
  • TEICOPLANIN-A2-2
KeywordsHydrolase/Antibiotic / site-selective catalyst / carrier protein approach / glycopeptide antibiotic / 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TEICOPLANIN-A2-2 / 2-amino-2-deoxy-beta-D-glucopyranose / alpha-D-mannopyranose / PHOSPHATE ION / 8-METHYLNONANOIC ACID / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Actinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsHan, S. / Le, B.V. / Hajare, H. / Baxter, R.H.G. / Miller, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-068649 United States
CitationJournal: J.Org.Chem. / Year: 2014
Title: X-ray Crystal Structure of Teicoplanin A2-2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy.
Authors: Han, S. / Le, B.V. / Hajare, H.S. / Baxter, R.H. / Miller, S.J.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Dec 25, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 2.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: TEICOPLANIN-A2-2
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,88710
Polymers20,7602
Non-polymers1,1278
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.116, 63.569, 138.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

21A-348-

HOH

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Components

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Protein/peptide / Protein , 2 types, 2 molecules BA

#1: Protein/peptide TEICOPLANIN-A2-2


Type: Glycopeptide / Class: Antibiotic / Mass: 1206.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinoplanes teichomyceticus (bacteria) / References: TEICOPLANIN-A2-2
#2: Protein Lysozyme


Mass: 19553.346 Da / Num. of mol.: 1 / Mutation: C54T/C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: D9IEF7, lysozyme

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Sugars , 3 types, 3 molecules

#3: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


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: 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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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: 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
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


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: 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 , 4 types, 137 molecules

#4: 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: TEICOPLANIN-A2-2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTEICOPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE ...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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.19 % / Description: THIN PLATES
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 19% PEG 3350 ,0.2 M sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.87→69.44 Å / Num. all: 20297 / Num. obs: 20297 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.099 / Net I/av σ(I): 15.7 / Net I/σ(I): 15.7
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.79 / % possible all: 99.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementResolution: 1.87→69.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.389 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22842 1081 5.1 %RANDOM
Rwork0.19382 ---
obs0.19555 20212 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0 Å20 Å2
2---1.18 Å2-0 Å2
3---2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.87→69.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 69 132 1598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021511
X-RAY DIFFRACTIONr_bond_other_d0.0010.021418
X-RAY DIFFRACTIONr_angle_refined_deg1.5772.0612048
X-RAY DIFFRACTIONr_angle_other_deg0.82533232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02360
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_it2.062.867700
X-RAY DIFFRACTIONr_mcbond_other2.0582.867699
X-RAY DIFFRACTIONr_mcangle_it2.8814.273872
X-RAY DIFFRACTIONr_mcangle_other2.8814.273873
X-RAY DIFFRACTIONr_scbond_it3.1993.333811
X-RAY DIFFRACTIONr_scbond_other3.1953.333811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8674.8551176
X-RAY DIFFRACTIONr_long_range_B_refined6.78930.791493
X-RAY DIFFRACTIONr_long_range_B_other6.71330.5531444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.874→1.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 90 -
Rwork0.323 1423 -
obs--96.8 %

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