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- PDB-6d17: Crystal structure of KPC-2 complexed with compound 3 -

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Basic information

Entry
Database: PDB / ID: 6d17
TitleCrystal structure of KPC-2 complexed with compound 3
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE inhibitor / beta-lactamase / carbapenemase / phosphonate / inhibitor / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-VKE / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103158-04 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,1833
Polymers30,8071
Non-polymers3762
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.480, 59.400, 77.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

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Components

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


Mass: 30806.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-VKE / [(6-oxo-2H,6H-[1,3]dioxolo[4,5-g][1]benzopyran-8-yl)methyl]phosphonic acid


Mass: 284.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% (v/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.45→56.48 Å / Num. obs: 46956 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Rsym value: 0.049 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.45-1.533.20.43566830.8530.0150.030.02698.6
4.59-56.483.70.02616120.9990.0230.0450.03898

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.43 Å47.24 Å
Translation5.43 Å47.24 Å

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Processing

Software
NameVersionClassification
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.8.0phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UL8

5ul8


Resolution: 1.45→47.239 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.66 / Phase error: 18.46
RfactorNum. reflection% reflection
Rfree0.1931 4296 4.87 %
Rwork0.1535 --
obs0.1554 46900 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.73 Å2 / Biso mean: 25.9966 Å2 / Biso min: 12.28 Å2
Refinement stepCycle: final / Resolution: 1.45→47.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 25 310 2351
Biso mean--28.99 40.84 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.3471300.2982593272391
1.4665-1.48370.33771090.29192718282794
1.4837-1.50180.30421560.26062647280396
1.5018-1.52080.30721610.25212776293798
1.5208-1.54090.28191910.24012746293799
1.5409-1.5620.2441320.21822818295098
1.562-1.58430.24091670.18532787295499
1.5843-1.60790.24391510.17292874302599
1.6079-1.63310.23081320.16152805293799
1.6331-1.65980.13681170.1462856297399
1.6598-1.68850.22311590.14982789294899
1.6885-1.71920.20031390.15482837297699
1.7192-1.75220.19871210.15362827294899
1.7522-1.7880.1841480.15542794294299
1.788-1.82690.19671260.16042875300199
1.8269-1.86940.21221570.15852807296499
1.8694-1.91610.21381210.15982863298499
1.9161-1.96790.22161580.14022784294299
1.9679-2.02580.16841900.14062767295799
2.0258-2.09120.18641550.14252827298299
2.0912-2.1660.19721620.13822814297699
2.166-2.25270.18431430.13452809295299
2.2527-2.35520.23081300.14142861299199
2.3552-2.47940.18421190.14782833295299
2.4794-2.63470.18361480.14472834298299
2.6347-2.83810.16461310.148628592990100
2.8381-3.12370.19011550.15482794294998
3.1237-3.57550.16871380.1432732287097
3.5755-4.50420.15391030.13142870297399
4.5042-47.26420.18691470.16742767291497

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