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- PDB-3mzf: Structure of penicillin-binding protein 5 from E. coli: imipenem ... -

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Basic information

Entry
Database: PDB / ID: 3mzf
TitleStructure of penicillin-binding protein 5 from E. coli: imipenem 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 / beta-lactamase activity / 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 / beta-lactamase activity / 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-IM2 / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 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 1.2Aug 31, 2011Group: Other
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Jul 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 1.5Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,2353
Polymers39,8411
Non-polymers3932
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.78, 50.35, 84.29
Angle α, β, γ (deg.)90.00, 120.16, 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) / Strain (production host): MC1061
References: UniProt: P0AEB2, serine-type D-Ala-D-Ala carboxypeptidase, beta-lactamase
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33 Å / Num. all: 61886 / Num. obs: 61886 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 40.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4880 / Rsym value: 0.488 / % possible all: 76.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NZO

1nzo


Resolution: 1.5→32.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.01 / SU ML: 0.051 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3123 5.1 %RANDOM
Rwork0.188 ---
all0.189 61823 --
obs0.189 61823 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.41 Å2
2---0.56 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 26 369 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222958
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9624003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5065367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0725.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5515527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2261517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022236
X-RAY DIFFRACTIONr_nbd_refined0.1930.21353
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.227
X-RAY DIFFRACTIONr_mcbond_it1.0211.51873
X-RAY DIFFRACTIONr_mcangle_it1.49622946
X-RAY DIFFRACTIONr_scbond_it4.44331216
X-RAY DIFFRACTIONr_scangle_it3.9484.51057
X-RAY DIFFRACTIONr_rigid_bond_restr5.09533089
X-RAY DIFFRACTIONr_sphericity_free3.3753369
X-RAY DIFFRACTIONr_sphericity_bonded3.3732904
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 185 -
Rwork0.272 3304 -
obs-3489 74.3 %

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