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- PDB-2jch: Structural and mechanistic basis of penicillin binding protein in... -

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Basic information

Entry
Database: PDB / ID: 2jch
TitleStructural and mechanistic basis of penicillin binding protein inhibition by lactivicins
ComponentsPENICILLIN-BINDING PROTEIN 1B
KeywordsDRUG-BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME / CELL WALL / PEPTIDOGLYCAN / GAMMA LACTAM ANTIBIOTICS / BINDING PROTEIN
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / proteolysis / extracellular region / membrane
Similarity search - Function
Rossmann fold - #12800 / Penicillin-binding protein 2a (Domain 2) - #40 / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase ...Rossmann fold - #12800 / Penicillin-binding protein 2a (Domain 2) - #40 / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PL7 / peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMacheboeuf, P. / Fisher, D.S. / Brown, T.J. / Zervosen, A. / Luxen, A. / Joris, B. / Dessen, A. / Schofield, C.J.
CitationJournal: Nat.Chem.Biol. / Year: 2007
Title: Structural and Mechanistic Basis of Penicillin-Binding Protein Inhibition by Lactivicins
Authors: Macheboeuf, P. / Fisher, D.S. / Brown, T.J. / Zervosen, A. / Luxen, A. / Joris, B. / Dessen, A. / Schofield, C.J.
History
DepositionDec 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0045
Polymers78,4281
Non-polymers5764
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.840, 143.580, 97.440
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-1791-

CL

21A-2037-

HOH

31A-2071-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PENICILLIN-BINDING PROTEIN 1B


Mass: 78428.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-791 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O70038

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Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PL7 / (2E)-2-({(2S)-2-CARBOXY-2-[(PHENOXYACETYL)AMINO]ETHOXY}IMINO)PENTANEDIOIC ACID / PHENYLACETYL LACTIVICIN


Mass: 382.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 73 TO SER ENGINEERED RESIDUE IN CHAIN A, LEU 123 TO MET ...ENGINEERED RESIDUE IN CHAIN A, ALA 73 TO SER ENGINEERED RESIDUE IN CHAIN A, LEU 123 TO MET ENGINEERED RESIDUE IN CHAIN A, LYS 158 TO ASN ENGINEERED RESIDUE IN CHAIN A, ARG 162 TO PRO ENGINEERED RESIDUE IN CHAIN A, ARG 336 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 687 TO GLN
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 67.7 % / Description: NONE
Crystal growpH: 7 / Details: 50 MM HEPES PH 7 3.2 M NACL 0.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: May 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→19.9 Å / Num. obs: 29294 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BG1

2bg1


Resolution: 2.4→85.13 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.898 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1434 4.9 %RANDOM
Rwork0.203 ---
obs0.206 27860 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2---0.04 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→85.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 36 147 3733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3981.9845001
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2995466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16825.089169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.09415558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5371515
X-RAY DIFFRACTIONr_chiral_restr0.1560.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022827
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.21695
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22390
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4740.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3211.52374
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1823665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.34731573
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8634.51332
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 107
Rwork0.258 1895

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