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- PDB-6b1x: Crystal structure KPC-2 beta-lactamase complexed with WCK 5153 by... -

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Basic information

Entry
Database: PDB / ID: 6b1x
TitleCrystal structure KPC-2 beta-lactamase complexed with WCK 5153 by soaking
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-C9D / CITRIC ACID / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)58,33714
Polymers56,6982
Non-polymers1,64012
Water8,647480
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2318
Polymers28,3491
Non-polymers8827
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)29,1076
Polymers28,3491
Non-polymers7585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.493, 37.436, 82.235
Angle α, β, γ (deg.)92.300, 90.210, 95.080
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-C9D / (2S,5R)-1-formyl-N'-[(3R)-pyrrolidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide / open form - WCK 5153


Mass: 379.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 34.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: of 20% PEG 6000, 100 mM citrate pH 4.0, 100 mM KSCN, 10 mM CdCl2, and 10mM WCK 5153.
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: 1.45→37.26 Å / Num. obs: 67132 / % possible obs: 92.6 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.03 / Rrim(I) all: 0.042 / Net I/σ(I): 15.2 / Num. measured all: 132820 / Scaling rejects: 0
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.187 / Num. unique obs: 2315 / CC1/2: 0.903 / Rpim(I) all: 0.187 / Rrim(I) all: 0.264 / % possible all: 64.7

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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: 1.45→34.46 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.076 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 3375 5 %RANDOM
Rwork0.1454 ---
obs0.1467 63748 92.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.64 Å2 / Biso mean: 10.922 Å2 / Biso min: 4.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.45→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 108 480 4565
Biso mean--15.57 23.27 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024250
X-RAY DIFFRACTIONr_bond_other_d0.0030.024052
X-RAY DIFFRACTIONr_angle_refined_deg2.3521.985787
X-RAY DIFFRACTIONr_angle_other_deg1.0653.0069302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49823.353170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09215648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0651533
X-RAY DIFFRACTIONr_chiral_restr0.3340.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214844
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02951
LS refinement shellResolution: 1.451→1.489 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 164 -
Rwork0.189 3474 -
all-3638 -
obs--67.87 %

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