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- PDB-8jb7: Crystal structure of CMY-185 -

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Basic information

Entry
Database: PDB / ID: 8jb7
TitleCrystal structure of CMY-185
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / CMY-2-like
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKawai, A. / Doi, Y.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI151362 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI104895 United States
Japan Society for the Promotion of Science (JSPS)23K06267 Japan
CitationJournal: Mbio / Year: 2024
Title: Structural insights into the molecular mechanism of high-level ceftazidime-avibactam resistance conferred by CMY-185.
Authors: Kawai, A. / Shropshire, W.C. / Suzuki, M. / Borjan, J. / Aitken, S.L. / Bachman, W.C. / McElheny, C.L. / Bhatti, M.M. / Shields, R.K. / Shelburne, S.A. / Doi, Y.
History
DepositionMay 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1554
Polymers79,9632
Non-polymers1922
Water19,4561080
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0782
Polymers39,9821
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area14670 Å2
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0782
Polymers39,9821
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.846, 89.687, 104.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 39981.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This CMY-185 protein is a N-terminus signal peptide truncated mutant (truncated residues: 1-22) of WCB91330.1
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CMY-185 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 20000, 0.1 M Tris-HCl (pH 8.5) and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→45.1 Å / Num. obs: 163856 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 14.05 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.42
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 26083 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→39.1 Å / SU ML: 0.1277 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.0512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1772 8188 5 %
Rwork0.139 155573 -
obs0.1409 163761 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.38 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 10 1080 6646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086180
X-RAY DIFFRACTIONf_angle_d0.94028506
X-RAY DIFFRACTIONf_chiral_restr0.0859902
X-RAY DIFFRACTIONf_plane_restr0.00781123
X-RAY DIFFRACTIONf_dihedral_angle_d12.9422241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.25132580.21954907X-RAY DIFFRACTION95.31
1.37-1.380.23322730.19055168X-RAY DIFFRACTION99.91
1.38-1.40.23792700.18875146X-RAY DIFFRACTION99.85
1.4-1.420.23762680.16995120X-RAY DIFFRACTION99.85
1.42-1.440.19992710.15455152X-RAY DIFFRACTION99.96
1.44-1.460.20682700.14885125X-RAY DIFFRACTION99.89
1.46-1.480.20062710.14525159X-RAY DIFFRACTION99.93
1.48-1.50.19962720.1385153X-RAY DIFFRACTION99.87
1.5-1.520.16882690.13645124X-RAY DIFFRACTION99.98
1.52-1.550.19952740.13645181X-RAY DIFFRACTION99.82
1.55-1.570.19752710.12815147X-RAY DIFFRACTION99.96
1.57-1.60.15792720.1185173X-RAY DIFFRACTION99.89
1.6-1.630.1772710.12015150X-RAY DIFFRACTION99.91
1.63-1.670.17232730.12685175X-RAY DIFFRACTION99.96
1.67-1.70.17292700.12945143X-RAY DIFFRACTION99.96
1.7-1.740.1852730.12675178X-RAY DIFFRACTION99.91
1.74-1.790.16362720.12215166X-RAY DIFFRACTION99.91
1.79-1.830.17112730.12295193X-RAY DIFFRACTION99.96
1.83-1.890.14662720.11725157X-RAY DIFFRACTION99.82
1.89-1.950.15952730.12185192X-RAY DIFFRACTION99.96
1.95-2.020.16122720.12765181X-RAY DIFFRACTION99.93
2.02-2.10.14852740.12945208X-RAY DIFFRACTION99.98
2.1-2.190.1592740.12785200X-RAY DIFFRACTION99.98
2.19-2.310.16122750.12865229X-RAY DIFFRACTION99.98
2.31-2.460.16442750.13995211X-RAY DIFFRACTION99.98
2.46-2.640.19112760.15175249X-RAY DIFFRACTION99.93
2.64-2.910.18322760.15455247X-RAY DIFFRACTION99.91
2.91-3.330.19272790.15185296X-RAY DIFFRACTION99.91
3.33-4.20.16752800.13075322X-RAY DIFFRACTION100
4.2-39.10.18442910.14725521X-RAY DIFFRACTION99.71

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