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- PDB-5kmu: CTX-M-9 beta lactamase mutant - T165W -

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Basic information

Entry
Database: PDB / ID: 5kmu
TitleCTX-M-9 beta lactamase mutant - T165W
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase / ESBL
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLatallo, M. / Faham, S. / Kasson, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
The Hartwell FoundationIndividual Biomedical Research Award United States
CitationJournal: Chem Sci / Year: 2017
Title: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme.
Authors: Latallo, M.J. / Cortina, G.A. / Faham, S. / Nakamoto, R.K. / Kasson, P.M.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _software.classification
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6999
Polymers30,9651
Non-polymers7348
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.743, 42.212, 68.035
Angle α, β, γ (deg.)90.00, 104.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 30965.244 Da / Num. of mol.: 1 / Mutation: T165W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9a, blaCTX-M-9, blaCTX-M-9b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 0.7 M potassium phosphate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97121 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 1.8→32.95 Å / Num. obs: 20959 / % possible obs: 95.52 % / Redundancy: 6.7 % / Net I/σ(I): 17.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Cootmodel building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.461 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.113
Details: Hydrogens were added and refined using a riding model.
RfactorNum. reflection% reflectionSelection details
Rfree0.18426 1078 5.1 %RANDOM
Rwork0.15949 ---
obs0.1608 19869 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0 Å2-0.6 Å2
2--1.76 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 42 137 2128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022050
X-RAY DIFFRACTIONr_bond_other_d0.0010.021972
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9752791
X-RAY DIFFRACTIONr_angle_other_deg0.73534525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29124.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09415330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6071516
X-RAY DIFFRACTIONr_chiral_restr0.0610.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 41 -
Rwork0.207 1101 -
obs--71.15 %
Refinement TLS params.Method: refined / Origin x: -6.857 Å / Origin y: 5.718 Å / Origin z: -18.084 Å
111213212223313233
T0.0087 Å2-0.0003 Å20.001 Å2-0.0012 Å20.0007 Å2--0.003 Å2
L0.2671 °20.0119 °20.0465 °2-0.1659 °20.0306 °2--0.1822 °2
S-0.0057 Å °-0.0115 Å °-0.0091 Å °0.0025 Å °0.0057 Å °0.004 Å °0.0011 Å °0.0072 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 288
2X-RAY DIFFRACTION1A301 - 308
3X-RAY DIFFRACTION1A401 - 537

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