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- PDB-6mnp: Crystal structure of KPC-2 with compound 6 -

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Basic information

Entry
Database: PDB / ID: 6mnp
TitleCrystal structure of KPC-2 with compound 6
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/INHIBITOR / Carbapenemase / tetrazole / inhibitor / complex / 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-1CE / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.202 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery.
Authors: Torelli, N.J. / Akhtar, A. / DeFrees, K. / Jaishankar, P. / Pemberton, O.A. / Zhang, X. / Johnson, C. / Renslo, A.R. / Chen, Y.
History
DepositionOct 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 1.4Oct 23, 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)31,7645
Polymers30,8071
Non-polymers9574
Water36020
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)56.347, 59.768, 77.094
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-410-

HOH

21A-420-

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-1CE / 3-(1H-tetrazol-5-ylmethyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one


Mass: 288.328 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H12N6OS / 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: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13530 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.072 / Rrim(I) all: 0.155 / Χ2: 1.082 / Net I/σ(I): 6.8 / Num. measured all: 66050
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2440.8066410.6820.4450.9250.91899.2
2.24-2.284.10.7336720.7890.3990.8380.89199.3
2.28-2.3240.6436710.7910.3610.7410.87199
2.32-2.374.60.6886430.8030.3620.780.8498.9
2.37-2.425.20.6456770.870.3220.7230.81599.9
2.42-2.485.40.5216760.9250.2590.5840.91999.1
2.48-2.545.40.4656580.9390.2290.520.94299.8
2.54-2.615.40.4276680.9520.2110.4781.08299.4
2.61-2.695.30.3776720.9310.1890.4231.109100
2.69-2.775.40.3096810.9580.1530.3471.251100
2.77-2.875.20.2776670.9470.1390.3111.12399.3
2.87-2.994.80.2176760.9750.1160.2471.15698.4
2.99-3.124.90.1946750.9760.10.2191.38699.6
3.12-3.295.40.1426810.990.0710.161.2999.4
3.29-3.495.30.1286720.9870.0660.1451.44798.8
3.49-3.764.90.1096820.9830.0580.1241.20598.8
3.76-4.144.60.0936850.9850.0520.1071.19498.1
4.14-4.744.20.0836700.9870.0470.0961.07896.3
4.74-5.9750.0847130.9870.0440.0951.0199.2
5.97-504.50.0767500.9870.0430.0880.93597.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.38 Å40.78 Å
Translation6.38 Å40.78 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3228refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 2.202→47.236 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 1337 9.92 %
Rwork0.2261 12135 -
obs0.231 13472 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.29 Å2 / Biso mean: 45.8964 Å2 / Biso min: 28.06 Å2
Refinement stepCycle: final / Resolution: 2.202→47.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 66 20 2072
Biso mean--59.02 40.03 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2019-2.28060.38451250.30291122124793
2.2806-2.37190.33381330.28231187132099
2.3719-2.47980.31161340.25141216135099
2.4798-2.61060.32161290.26241195132499
2.6106-2.77410.30811310.25912201351100
2.7741-2.98830.32981390.26751215135499
2.9883-3.28890.29391340.24471213134799
3.2889-3.76470.28041260.22371241136799
3.7647-4.74240.22161410.18971210135197
4.7424-47.24640.24411450.19961316146198

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