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- PDB-3bec: Crystal structure of E. coli penicillin-binding protein 5 in comp... -

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Basic information

Entry
Database: PDB / ID: 3bec
TitleCrystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic cephalosporin
ComponentsPenicillin-binding protein 5
KeywordsHYDROLASE / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE / DESIGNED CEPHALOSPORIN / Cell shape / Cell wall biogenesis/degradation / Inner membrane / Membrane / Protease
Function / homology
Function and homology information


peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape / outer membrane-bounded periplasmic space / cell division / protein homodimerization activity / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase ...Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-HJ2 / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsPowell, A.J. / Davies, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle
Authors: Sauvage, E. / Powell, A.J. / Heilemann, J. / Josephine, H.R. / Charlier, P. / Davies, C. / Pratt, R.F.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 1.3Oct 30, 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 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5996
Polymers39,8411
Non-polymers7585
Water4,684260
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.500, 50.500, 85.400
Angle α, β, γ (deg.)90.00, 121.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Penicillin-binding protein 5 / DD- peptidase / DD-carboxypeptidase / Beta-lactamase / D-alanyl-D-alanine carboxypeptidase dacA / PBP-5


Mass: 39841.117 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 30-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dacA, pfv / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061
References: UniProt: P0AEB2, serine-type D-Ala-D-Ala carboxypeptidase, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HJ2 / (2R)-2-[(R)-{[(6S)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 389.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS' STATE THAT THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE ...THE AUTHORS' STATE THAT THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX AMINO ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE TO READ-THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST 29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE AND IS NOT PRESENT IN THIS CONSTRUCT.

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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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris pH 8.0, 8% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2006
RadiationMonochromator: Double crystal monochromator Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.6→41 Å / Num. all: 51428 / Num. obs: 51428 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.8 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NZO

1nzo


Resolution: 1.6→40.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.538 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21473 2602 5.1 %RANDOM
Rwork0.19215 ---
obs0.19328 48813 97.15 %-
all-51415 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.458 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.68 Å2
2--0.35 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 37 260 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222834
X-RAY DIFFRACTIONr_bond_other_d0.0010.021926
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9733821
X-RAY DIFFRACTIONr_angle_other_deg0.87234716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31924.921126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.971515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023127
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined0.2010.2533
X-RAY DIFFRACTIONr_nbd_other0.1910.21987
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21389
X-RAY DIFFRACTIONr_nbtor_other0.0860.21436
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1371.51807
X-RAY DIFFRACTIONr_mcbond_other0.4051.5723
X-RAY DIFFRACTIONr_mcangle_it1.64622807
X-RAY DIFFRACTIONr_scbond_it2.3231179
X-RAY DIFFRACTIONr_scangle_it3.2764.51014
X-RAY DIFFRACTIONr_rigid_bond_restr1.54635274
X-RAY DIFFRACTIONr_sphericity_free4.7783260
X-RAY DIFFRACTIONr_sphericity_bonded2.32334713
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 142 -
Rwork0.272 2901 -
obs--78.29 %

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