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- PDB-3mze: Structure of penicillin-binding protein 5 from E.coli: cefoxitin ... -

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Basic information

Entry
Database: PDB / ID: 3mze
TitleStructure of penicillin-binding protein 5 from E.coli: cefoxitin acyl-enzyme complex
ComponentsD-alanyl-D-alanine carboxypeptidase dacA
KeywordsHYDROLASE/ANTIBIOTIC / BETA-LACTAM ANTIBIOTIC / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE / HYDROLASE / HYDROLASE-ANTIBIOTIC complex
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-1QL / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsNicola, G. / Tomberg, J. / Pratt, R.F. / Nicholas, R.A. / Davies, C.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structures of covalent complexes of beta-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity
Authors: Nicola, G. / Tomberg, J. / Pratt, R.F. / Nicholas, R.A. / Davies, C.
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Sep 12, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_host_org_strain / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.3Oct 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

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Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase dacA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6396
Polymers39,8411
Non-polymers7985
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.42, 50.34, 84.23
Angle α, β, γ (deg.)90.00, 120.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39841.117 Da / Num. of mol.: 1 / Fragment: Soluble construct
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0632, dacA, JW0627, pfv / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEB2, serine-type D-Ala-D-Ala carboxypeptidase, beta-lactamase
#2: Chemical ChemComp-1QL / (2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefoxitin, bound form


Mass: 429.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O7S2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THIS IS A SOLUBLE CONSTRUCT OF PBP 5. THE FIRST 29 AMINO ACIDS OF THE PROTEIN, ...AUTHORS STATE THAT THIS IS A SOLUBLE CONSTRUCT OF PBP 5. THE FIRST 29 AMINO ACIDS OF THE PROTEIN, WHICH ENCODE THE SIGNAL SEQUENCE, ARE NOT INCLUDED. THE LAST 17 AMINO ACIDS OF THE WILD-TYPE SEQUENCE ARE ALSO ABSENT AND ARE REPLACED BY SIX NON-NATIVE AMINO ACIDS (GDPVID - INTRODUCED BY READ-THROUGH TO THE STOP CODON)

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 MM TRIS PH 7.0, 8 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2001 / Details: osmic blue
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→54 Å / Num. all: 23307 / Num. obs: 23307 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 5.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.371 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NZO

1nzo


Resolution: 2.1→54 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.321 / SU ML: 0.171 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1197 5.2 %RANDOM
Rwork0.225 ---
all0.228 23241 --
obs0.228 23241 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.1 Å2
2---0.93 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 48 118 2879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222826
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9733816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65625126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32115490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5071515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022121
X-RAY DIFFRACTIONr_nbd_refined0.2050.21246
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.27
X-RAY DIFFRACTIONr_mcbond_it0.681.51790
X-RAY DIFFRACTIONr_mcangle_it1.16722806
X-RAY DIFFRACTIONr_scbond_it1.6331162
X-RAY DIFFRACTIONr_scangle_it2.5644.51010
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 84 -
Rwork0.256 1605 -
obs-1689 100 %

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