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- PDB-6b1y: Crystal structure KPC-2 beta-lactamase complexed with WCK 5153 by... -

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Basic information

Entry
Database: PDB / ID: 6b1y
TitleCrystal structure KPC-2 beta-lactamase complexed with WCK 5153 by co-crystallization
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE Inhibitor / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
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, 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-CD7 / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Authorsvan den Akker, F. / Nguyen, N.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Wockhardt United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, ...Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234.
Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / ...Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / Patil, V. / Yeole, R. / Bhagwat, S.S. / Patel, M.V. / van den Akker, F. / Bonomo, R.A.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,19613
Polymers56,6982
Non-polymers1,49811
Water6,035335
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9545
Polymers28,3491
Non-polymers6054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2428
Polymers28,3491
Non-polymers8937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.529, 37.349, 82.070
Angle α, β, γ (deg.)87.660, 89.710, 84.310
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 28348.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-CD7 / (2S,5Z)-1-formyl-5-imino-N'-[(3R)-1-(sulfooxy)pyrrolidine-3-carbonyl]piperidine-2-carbohydrazide / open form - WCK 5153


Mass: 377.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsThe covalently bound inhibitor becomes desulfated during the co-crystallization process

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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: 1.86 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 200mM Lithium sulfate, 100mM sodium acetate pH 4.4-4.6, and 28-31% PEG8000. Protein to inhibitor molar ratio of 1 is to 10 and KPC-2 concentration was 10 mg/mL
PH range: 4.4 - 4.6 / Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12708 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12708 Å / Relative weight: 1
ReflectionResolution: 1.8→37.13 Å / Num. obs: 35965 / % possible obs: 95.5 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Rrim(I) all: 0.065 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2 % / Rmerge(I) obs: 0.272 / Num. unique obs: 2083 / CC1/2: 0.8 / Rpim(I) all: 0.272 / Rrim(I) all: 0.384 / % possible all: 92

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.13 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.86 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1799 5 %RANDOM
Rwork0.1486 ---
obs0.151 34166 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.38 Å2 / Biso mean: 14.148 Å2 / Biso min: 5.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0.01 Å2
2---0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3975 0 77 335 4387
Biso mean--24.05 21.41 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024133
X-RAY DIFFRACTIONr_bond_other_d0.0030.023913
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9755632
X-RAY DIFFRACTIONr_angle_other_deg1.0973.0058973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20223.537164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9215623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0431530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214715
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02925
LS refinement shellResolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 137 -
Rwork0.219 2461 -
all-2598 -
obs--92.42 %

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