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- PDB-2bg1: Active site restructuring regulates ligand recognition in classA ... -

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Basic information

Entry
Database: PDB / ID: 2bg1
TitleActive site restructuring regulates ligand recognition in classA Penicillin-binding proteins (PBPs)
ComponentsPENICILLIN-BINDING PROTEIN 1B
KeywordsPEPTIDOGLYCAN / PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME / CELL WALL
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding
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 / DD-peptidase/beta-lactamase superfamily ...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
peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsMacheboeuf, P. / Di Guilmi, A.M. / Job, V. / Vernet, T. / Dideberg, O. / Dessen, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Active Site Restructuring Regulates Ligand Recognition in Class a Penicillin-Binding Proteins
Authors: Macheboeuf, P. / Di Guilmi, A.M. / Job, V. / Vernet, T. / Dideberg, O. / Dessen, A.
History
DepositionDec 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,2743
Polymers54,1431
Non-polymers1322
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.331, 149.447, 97.976
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-2178-

HOH

21A-2208-

HOH

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 1B / PBP1B


Mass: 54142.930 Da / Num. of mol.: 1
Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125 AND RESIDUES 323-791
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O70038, UniProt: Q7CRA4*PLUS, peptidoglycan glycosyltransferase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUATION CHAIN A ARG 336 GLN, ARG 686 GLN AND ARG 687 GLN
Sequence detailsSTREPTOCOCCUS PNEUMONIAE R6 COMPLETE GENOME

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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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50MM HEPES PH 7.0, 0.8M SO4(NH4)2, 2.8M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9794
DetectorDate: Jun 18, 2003 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→24.7 Å / Num. obs: 56963 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2343068.7 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 5798 10.2 %RANDOM
Rwork0.2019 ---
obs0.2019 56963 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.523 Å2 / ksol: 0.326342 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.055 Å20 Å20 Å2
2--2.682 Å20 Å2
3----1.627 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 6 386 3916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004795
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.17778
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 985 10.5 %
Rwork0.212 8378 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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