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- PDB-3m6b: Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct... -

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Basic information

Entry
Database: PDB / ID: 3m6b
TitleCrystal Structure of the Ertapenem Pre-isomerized Covalent Adduct with TB B-lactamase
ComponentsBeta-lactamase
KeywordsHydrolase/Antibiotic / alpha-beta structure / Antibiotic resistance / Cell membrane / Hydrolase / Lipoprotein / Membrane / Palmitate / 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-1RG / PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTremblay, L.W. / Fan, F. / Blanchard, J.S.
CitationJournal: Biochemistry / Year: 2010
Title: Biochemical and structural characterization of Mycobacterium tuberculosis beta-lactamase with the carbapenems ertapenem and doripenem.
Authors: Tremblay, L.W. / Fan, F. / Blanchard, J.S.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 16, 2012Group: Non-polymer description / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,4185
Polymers28,2731
Non-polymers1,1454
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.657, 67.922, 75.546
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, Rv2068c, MT2128, MTCY49.07c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
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-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4.1
Details: 0.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K

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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: Jan 21, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 63485 / Num. obs: 63485 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.4
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4388 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3DWZ

3dwz


Resolution: 1.3→26.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.384 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.176 3222 5.1 %RANDOM
Rwork0.147 ---
obs0.149 60263 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.73 Å2 / Biso mean: 13.287 Å2 / Biso min: 4.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati sigma a0.046 Å0.048 Å
Refinement stepCycle: LAST / Resolution: 1.3→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 61 297 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222109
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9942887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29823.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50815309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3411520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211631
X-RAY DIFFRACTIONr_mcbond_it1.1981.51336
X-RAY DIFFRACTIONr_mcangle_it1.95922141
X-RAY DIFFRACTIONr_scbond_it3.0093773
X-RAY DIFFRACTIONr_scangle_it4.4514.5743
X-RAY DIFFRACTIONr_rigid_bond_restr1.29232109
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 235 -
Rwork0.265 4388 -
all-4623 -
obs-4388 99.96 %

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