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- PDB-6m5h: A class C beta-lactamase mutant - Y150F -

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Basic information

Entry
Database: PDB / ID: 6m5h
TitleA class C beta-lactamase mutant - Y150F
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 10, 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


Theoretical massNumber of molelcules
Total (without water)40,6971
Polymers40,6971
Non-polymers00
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.150, 59.980, 55.100
Angle α, β, γ (deg.)90.000, 111.310, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
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: Photon Factory / Beamline: BL-5A / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 430004 / % possible obs: 96.7 % / Redundancy: 3.35 % / Rsym value: 0.01 / Net I/σ(I): 6.54
Reflection shellResolution: 0.98→4.39 Å / Num. unique obs: 30255 / CC1/2: 0.061

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K8X

6k8x


Resolution: 1.2→32.99 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2066 --
Rwork0.1775 --
obs-121606 98.68 %
Displacement parametersBiso mean: 14.51 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 0 383 3152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972830
X-RAY DIFFRACTIONf_angle_d1.14623848
X-RAY DIFFRACTIONf_chiral_restr0.0988441
X-RAY DIFFRACTIONf_plane_restr0.0082491
X-RAY DIFFRACTIONf_dihedral_angle_d13.81131032
LS refinement shellResolution: 1.2→1.255 Å
RfactorNum. reflection% reflection
Rfree0.25377 --
Rwork0.2403 --
obs-14777 97 %

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