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- PDB-6m5p: A class C beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6m5p
TitleA class C beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / nucleotide binding
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-MER / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBae, D.W. / Jung, Y.E. / Cha, S.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2015M1A5A1037480 Korea, Republic Of
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Novel inhibition mechanism of carbapenems on the ACC-1 class C beta-lactamase.
Authors: Bae, D.W. / Jung, Y.E. / Jeong, B.G. / Cha, S.S.
History
DepositionMar 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)41,0832
Polymers40,6971
Non-polymers3851
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint0 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.918, 60.233, 54.518
Angle α, β, γ (deg.)90.000, 110.710, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Beta-lactamase


Mass: 40697.316 Da / Num. of mol.: 1 / Mutation: Y150F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla-ACC-1, acc-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XB24, beta-lactamase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 51.06 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 30% polyethylene glycol 1500, 0.1M sodium cacodylate (pH 5.5), 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 102328 / % possible obs: 94.1 % / Redundancy: 5.4 % / Rsym value: 0.068 / Net I/σ(I): 31.55
Reflection shellResolution: 1.25→3.39 Å / Num. unique obs: 4615 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
PHENIX1.11refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K8X

6k8x


Resolution: 1.25→34.461 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.1739 --
obs-102328 94.11 %
Displacement parametersBiso mean: 16.86 Å2
Refinement stepCycle: LAST / Resolution: 1.25→34.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 26 348 3110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01272822
X-RAY DIFFRACTIONf_angle_d0.99823842
X-RAY DIFFRACTIONf_chiral_restr0.0836443
X-RAY DIFFRACTIONf_plane_restr0.0057489
X-RAY DIFFRACTIONf_dihedral_angle_d15.27541011
LS refinement shellResolution: 1.25→1.294 Å
RfactorNum. reflection% reflection
Rfree0.2937 --
Rwork0.2725 --
obs-9368 86.85 %

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