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Basic information

Entry
Database: PDB / ID: 2xd5
TitleStructural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b
ComponentsPENICILLIN-BINDING PROTEIN 1B
KeywordsTRANSFERASE / CELL WALL / PEPTIDOGLYCAN SYNTHESIS / MULTIFUNCTIONAL ENZYME / PSEUDO-SUBSTRATE
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / proteolysis / metal ion binding / 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
N-BENZOYL-D-ALANINE / Penicillin-binding protein 1b
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMacheboeuf, P. / Lemaire, D. / Jamin, M. / Dideberg, O. / Dessen, A.
Citation
Journal: To be Published
Title: Structural Insights Into the Catalytic Mechanism and the Role of Streptococcus Pneumoniae Pbp1B
Authors: Macheboeuf, P. / Lemaire, D. / Jamin, M. / Dideberg, O. / Dessen, A.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Trapping of an Acyl-Enzyme Intermediate in a Penicillin-Binding Protein (Pbp)-Catalyzed Reaction.
Authors: Macheboeuf, P. / Lemaire, D. / Teller, N. / Martins, A.D.S. / Luxen, A. / Dideberg, O. / Jamin, M. / Dessen, A.
History
DepositionApr 29, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMay 26, 2010ID: 2JCI
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
B: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9358
Polymers108,2862
Non-polymers6496
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-42.2 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.800, 101.100, 145.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, 0.034, 0.001), (-0.032, -0.939, -0.342), (-0.011, -0.342, 0.94)
Vector: 0.46948, 0.72849, 0.09179)

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 1B


Mass: 54142.930 Da / Num. of mol.: 2 / Fragment: RESIDUES 323-791 / 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: Q7CRA4, Transferases; Acyltransferases; Aminoacyltransferases, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-S2D / N-BENZOYL-D-ALANINE


Type: D-peptide linking / Mass: 193.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 336 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ...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 ENGINEERED RESIDUE IN CHAIN B, ARG 336 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN B, 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: 3.36 Å3/Da / Density % sol: 63.07 % / Description: NONE
Crystal growpH: 7
Details: 50 MM HEPES, 3.2 M NACL, 0.8 M AMMONIUM SULFATE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→45.91 Å / Num. obs: 49863 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 11.46
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.05 / % possible all: 100

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Processing

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

2bg1


Resolution: 2.5→83.05 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.42 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.305 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2481 5 %RANDOM
Rwork0.181 ---
obs0.184 47382 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7209 0 30 250 7489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0227436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1821.94210106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0065944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8725.291344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.701151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3751528
X-RAY DIFFRACTIONr_chiral_restr0.220.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025715
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.23486
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.25105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2354
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1231.54796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87927471
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93733102
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4664.52635
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: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 152 -
Rwork0.253 3459 -
obs--99.9 %

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