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- PDB-3dwz: Meropenem Covalent Adduct with TB Beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 3dwz
TitleMeropenem Covalent Adduct with TB Beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / alpha-beta folded protein / protein-covalent adduct / Antibiotic resistance / Hydrolase / Lipoprotein / Membrane / Palmitate / Meropenem (open form) / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


: / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DWZ / PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTremblay, L.W. / Hugonnet, J.E. / Blanchard, J.S.
CitationJournal: Science / Year: 2009
Title: Meropenem-clavulanate is effective against extensively drug-resistant Mycobacterium tuberculosis
Authors: Hugonnet, J.E. / Tremblay, L.W. / Boshoff, H.I. / Barry, C.E. / Blanchard, J.S.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 2, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8484
Polymers28,2731
Non-polymers5753
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.852, 67.595, 75.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 28272.721 Da / Num. of mol.: 1 / Fragment: residues 43-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Ra / Gene: blaA, blaC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 cells
References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.1 M HEPES pH 7.4, 2 M ammonium di-hydrogen phosphate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2008
Details: vertically collimating mirror and a doubly focusing toroidal mirror
RadiationMonochromator: channel-cut Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→30.83 Å / Num. all: 24330 / Num. obs: 23819 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 12.988 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2249 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3cg5

3cg5


Resolution: 1.8→30.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.266 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19249 1165 4.9 %RANDOM
Rwork0.15242 ---
all0.1544 23819 --
obs0.1544 22449 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.988 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.115 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→30.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 36 337 2361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222061
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9872815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9395262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30223.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89615303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7591519
X-RAY DIFFRACTIONr_chiral_restr0.10.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021576
X-RAY DIFFRACTIONr_nbd_refined0.2290.21068
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.232
X-RAY DIFFRACTIONr_mcbond_it0.6961.51350
X-RAY DIFFRACTIONr_mcangle_it1.0622102
X-RAY DIFFRACTIONr_scbond_it1.9513803
X-RAY DIFFRACTIONr_scangle_it3.0864.5713
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 82 -
Rwork0.194 1580 -
obs--93.58 %

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