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- PDB-8jb8: Crystal structure of CMY-185 complex with ceftazidime -

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Basic information

Entry
Database: PDB / ID: 8jb8
TitleCrystal structure of CMY-185 complex with ceftazidime
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / CMY-2-like
Function / homologyACYLATED CEFTAZIDIME
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,9024
Polymers79,9632
Non-polymers9392
Water3,243180
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4512
Polymers39,9821
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4512
Polymers39,9821
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.143, 89.266, 104.757
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-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 20,000, 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, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→45.2 Å / Num. obs: 30373 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 37.68 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.96
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 4823 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.18 Å / SU ML: 0.2667 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 1519 5.01 %
Rwork0.1862 28800 -
obs0.1885 30319 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.34 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 62 180 5740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00555716
X-RAY DIFFRACTIONf_angle_d0.74157802
X-RAY DIFFRACTIONf_chiral_restr0.0468835
X-RAY DIFFRACTIONf_plane_restr0.00561001
X-RAY DIFFRACTIONf_dihedral_angle_d13.75572038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.30571350.24192565X-RAY DIFFRACTION98.86
2.48-2.570.28671360.24382578X-RAY DIFFRACTION99.82
2.57-2.670.28991340.23512542X-RAY DIFFRACTION99.78
2.67-2.790.27181380.21772625X-RAY DIFFRACTION99.96
2.79-2.940.25851370.21312584X-RAY DIFFRACTION99.96
2.94-3.120.26111370.21662619X-RAY DIFFRACTION99.96
3.12-3.360.2491370.20062592X-RAY DIFFRACTION99.93
3.36-3.70.21221380.17542626X-RAY DIFFRACTION99.86
3.7-4.240.21621390.1612631X-RAY DIFFRACTION99.78
4.24-5.340.20531400.15242665X-RAY DIFFRACTION99.89
5.34-45.180.1841480.16892773X-RAY DIFFRACTION99.25
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.595108852964.40504604212-1.794858101159.33958005304-4.082731846964.220758049880.531176874179-0.4900476181660.7190790917391.43759353314-0.3880293376610.541992999481-0.869439624709-0.0580483386249-0.04708852876580.491196971067-0.06015031744590.03000793611580.521799848735-0.07809334097690.384315381984-7.251282893393.1456702745-13.2956574397
22.894556019820.0629061341742-0.4631509498711.54268188823-0.1340124128651.40888276107-0.005860329750020.1375454634260.1825345160870.0687844782557-0.02612711052820.0304804399053-0.0508610097171-0.0399677749170.02952834229030.264489938162-0.0157659755919-0.05928258685310.3313737156990.01123655129640.280794798023-8.17274268241-0.963786792021-29.6057697723
33.97911049619-0.133872099177-1.698407509342.95879225978-0.3768822937392.485926427230.1664639169110.758088899543-0.193867489319-0.589790135026-0.390463405223-0.5767976007530.0516210423674-0.06570053372320.2466873613960.4511170731550.09154770053380.08905783835740.4281591360730.04322367680490.3988172869887.9197968178-12.9126674383-46.9367880767
41.81873512572-1.61744845178-0.2903649020084.409379736910.2546779468931.74188478830.1387590951650.214241281253-0.0829686115149-0.145798189672-0.07839402125280.265133821831-0.0210783635122-0.0769824313628-0.05398210333890.267676163148-0.0191951748813-0.01686270414430.3779540430980.03903640327790.283680002654-7.43221615624-3.93356527905-36.5146141277
53.64078454058-0.866752066658-1.402408929921.00332819977-0.8000659121543.46504270259-0.14047996627-0.00436382532876-0.06947268652560.261987913547-0.3089825985-0.28883259513-0.104053679683-0.01079190544190.3959958069970.4126841222970.00808783726428-0.03085963690240.4298147482890.1403197858070.5045708499378.76940820889-16.8780645664-26.3047521211
62.51880792324-1.36891679157-0.5233494541733.003800054420.06440742176181.04135350611-0.0922308070766-0.5014934603690.07776833913850.3969627499970.011477041331-0.19831195522-0.1162752194290.2007119838860.06252211337340.361756021867-0.0445256473064-0.03692469175030.4580635344930.04404724986480.3643586657630.108813212797-4.02395267858-22.0981163743
72.331714900161.687921564430.9632568771736.564584367153.76598965444.899501869190.251412696484-0.218809321825-0.412733565421.097443254110.0672134655952-0.5034230755910.6029149297910.362213682992-0.2943559406010.417243043849-0.022564404321-0.1147881497290.3330226612280.09346002946320.42282342946647.715436607511.4369501115-13.1458537219
81.78599430661-0.7485662260370.3208433455892.79354108396-0.6112345560461.167366935450.1125531366140.181425541806-0.00556025331803-0.120112875605-0.0840174612943-0.252012488490.0009941904228520.0119398033397-0.007153274920190.277241073501-0.002354624237410.01879973637910.2609786766930.0001042098703910.22596542411644.999384091920.8274444231-34.6856774576
93.90748305713-0.1625106307220.6150446449562.498172241990.1815920087131.821698798390.1076913073490.58827383244-0.0774841755378-0.524755379144-0.269007969570.09494405148570.0382763591336-0.04614230683340.1641549304550.4194130492350.08295702889160.006942058393260.325672326509-0.005476346483530.21736575532334.833351043625.3683502047-45.0822265882
101.39005712791-0.2717155407410.4341060899814.730089409830.7046718491441.220368929210.3716397316060.127474074776-0.0597641724656-0.22138749885-0.315741132662-0.4511318708280.2302469727180.00988477835982-0.08189069391790.3120092844940.05399956035020.03406315697410.298831280650.03529575413070.27549729827546.136867537713.2536885572-36.7355529645
114.00414829915-0.5998065762790.2782949090323.172596926320.3031433145313.098385212570.110856858571-0.223704476934-0.1636405168660.330591339585-0.172621340925-0.0441174192370.08676009087870.03564959601080.1078189850220.325186097221-0.0197615007373-0.03415198202650.1969065586560.001837831420320.24441569713136.597307352133.0201785403-27.4139042613
122.20681445821-1.931291934760.5076610254693.26007322706-1.220994024150.519010489071-0.0185247267175-0.08035653534720.1472275287570.445475612229-0.133820451169-0.045609489542-0.170194885862-0.1280427413450.166375466230.377477962477-0.06261953961070.01250709588270.290679181832-0.002180256571060.23546456689940.440420785418.8039979304-21.9669881226
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 23 )AA2 - 231 - 22
22chain 'A' and (resid 24 through 80 )AA24 - 8023 - 79
33chain 'A' and (resid 81 through 182 )AA81 - 18280 - 181
44chain 'A' and (resid 183 through 255 )AA183 - 255182 - 254
55chain 'A' and (resid 256 through 310 )AA256 - 310255 - 303
66chain 'A' and (resid 311 through 361 )AA311 - 361304 - 354
77chain 'B' and (resid 2 through 23 )BB2 - 231 - 22
88chain 'B' and (resid 24 through 98 )BB24 - 9823 - 97
99chain 'B' and (resid 99 through 192 )BB99 - 19298 - 191
1010chain 'B' and (resid 193 through 238 )BB193 - 238192 - 237
1111chain 'B' and (resid 239 through 310 )BB239 - 310238 - 302
1212chain 'B' and (resid 311 through 361 )BB311 - 361303 - 353

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