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- PDB-4s2i: CTX-M-15 in complex with Avibactam -

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Basic information

Entry
Database: PDB / ID: 4s2i
TitleCTX-M-15 in complex with Avibactam
ComponentsBeta-lactamase
KeywordsHydrolase/antibiotic / Hydrolase-antibiotic complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
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
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
CitationJournal: ACS Infect Dis / Year: 2015
Title: Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition.
Authors: King, D.T. / King, A.M. / Lal, S.M. / Wright, G.D. / Strynadka, N.C.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Non-polymer description
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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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)56,8124
Polymers56,2782
Non-polymers5352
Water9,836546
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4062
Polymers28,1391
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4062
Polymers28,1391
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.010, 60.650, 71.500
Angle α, β, γ (deg.)90.00, 104.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein behaves as a monomer in solution

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Components

#1: Protein Beta-lactamase /


Mass: 28138.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form, NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulphate, 0.1M MES pH 6.5, 30% PEG 5K MME, 5mM avibactam, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→34.7 Å / Num. all: 68014 / Num. obs: 65627 / % possible obs: 96.7 % / Biso Wilson estimate: 19.23 Å2
Reflection shellResolution: 1.6→1.69 Å / % possible all: 95.2

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.87 Å / Cor.coef. Fo:Fc: 0.9557 / Cor.coef. Fo:Fc free: 0.9431 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 3320 5.06 %RANDOM
Rwork0.1727 ---
obs0.174 65626 96.5 %-
all-68006 --
Displacement parametersBiso mean: 18.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.1288 Å20 Å20.3372 Å2
2--0.2747 Å20 Å2
3----1.4035 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 34 546 4463
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093989HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085416HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1396SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes581HARMONIC5
X-RAY DIFFRACTIONt_it3989HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion15.37
X-RAY DIFFRACTIONt_chiral_improper_torsion550SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6076SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2655 247 5.19 %
Rwork0.2448 4511 -
all0.2459 4758 -
obs--96.5 %
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)
10.69510.5018-0.05140.7958-0.18980.5879-0.01360.07640.0333-0.0370.01560.0012-0.0224-0.0192-0.0021-0.0276-0.00050.0092-0.0313-0.0016-0.04230.522212.765815.7774
20.93370.0450.00550.632-0.02470.5370.0346-0.03740.02670.0129-0.0149-0.07180.03840.0211-0.0197-0.0364-0.00410.0059-0.030.01-0.040314.010418.699651.6923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A27 - 288
2X-RAY DIFFRACTION2{ B|* }B28 - 288

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