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- PDB-3e2k: Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhi... -

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Basic information

Entry
Database: PDB / ID: 3e2k
TitleCrystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP)
Components
  • Beta-lactamase inhibitory proteinBeta-lactamase inhibitor protein
  • CarbapenemaseBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Beta-lactamase / Beta-lactamase inhibitor protein / protein-protein complex / BLIP / KPC-2 / Antibiotic resistance / Hydrolase / Plasmid / Secreted / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase ...Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase inhibitory protein / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHanes, M.S. / Jude, K.M. / Berger, J.M. / Bonomo, R.A. / Handel, T.M.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein
Authors: Hanes, M.S. / Jude, K.M. / Berger, J.M. / Bonomo, R.A. / Handel, T.M.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbapenemase
B: Carbapenemase
C: Beta-lactamase inhibitory protein
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)91,1004
Polymers91,1004
Non-polymers00
Water3,675204
1
A: Carbapenemase
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,5502
Polymers45,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-7 kcal/mol
Surface area16410 Å2
MethodPISA
2
B: Carbapenemase
C: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,5502
Polymers45,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-6 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.240, 76.198, 241.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbapenemase / Beta-lactamase / Class A carbapenemase / Beta-lactamase / Class A carbapenemase KPC-2


Mass: 27993.451 Da / Num. of mol.: 2 / Fragment: UNP residues 30-293 / Mutation: G175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPC-2, blaKPC-2 / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / Beta-lactamase inhibitor protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35804
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 8000, 4% ethylene glycol, 100mM citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2008
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 46315 / Num. obs: 46291 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.127
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.689 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.78 Å
Translation2.5 Å40.78 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.777 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 1.33 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2329 5.05 %
Rwork0.1903 --
obs0.1925 46130 99.53 %
all-46315 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.318 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 34.913 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å2-0 Å2
2--6.256 Å2-0 Å2
3----10.357 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 0 204 6514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056460
X-RAY DIFFRACTIONf_angle_d0.9518784
X-RAY DIFFRACTIONf_dihedral_angle_d15.4532232
X-RAY DIFFRACTIONf_chiral_restr0.062989
X-RAY DIFFRACTIONf_plane_restr0.0041144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13180.24551450.20892390X-RAY DIFFRACTION95
2.1318-2.17820.26651390.20642555X-RAY DIFFRACTION100
2.1782-2.22880.26781310.21342496X-RAY DIFFRACTION99
2.2288-2.28460.29381280.21272587X-RAY DIFFRACTION100
2.2846-2.34630.27071420.2062499X-RAY DIFFRACTION100
2.3463-2.41540.2421340.20262580X-RAY DIFFRACTION100
2.4154-2.49330.3021360.20272526X-RAY DIFFRACTION100
2.4933-2.58240.25031250.20972580X-RAY DIFFRACTION100
2.5824-2.68580.24331300.20782552X-RAY DIFFRACTION100
2.6858-2.8080.25931450.21282564X-RAY DIFFRACTION100
2.808-2.9560.29581360.222591X-RAY DIFFRACTION100
2.956-3.14110.27481500.21362563X-RAY DIFFRACTION100
3.1411-3.38360.22381220.20262600X-RAY DIFFRACTION100
3.3836-3.72390.23911390.1742618X-RAY DIFFRACTION100
3.7239-4.26220.18061440.16272617X-RAY DIFFRACTION100
4.2622-5.3680.18071410.15042665X-RAY DIFFRACTION100
5.368-40.78440.20741420.18492818X-RAY DIFFRACTION99

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