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- PDB-5uj3: Crystal structure of the KPC-2 beta-lactamase complexed with hydr... -

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Basic information

Entry
Database: PDB / ID: 5uj3
TitleCrystal structure of the KPC-2 beta-lactamase complexed with hydrolyzed cefotaxime
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/ANTIBIOTIC / carbapenemase / cefotaxime / beta-lactamase / complex / HYDROLASE-ANTIBIOTIC 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-CE4 / Carbapenem-hydrolyzing beta-lactamase KPC
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)4R01AI103158-04 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Molecular Basis of Substrate Recognition and Product Release by the Klebsiella pneumoniae Carbapenemase (KPC-2).
Authors: Pemberton, O.A. / Zhang, X. / Chen, Y.
History
DepositionJan 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)31,7264
Polymers30,8071
Non-polymers9193
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint0 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 58.780, 76.840
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-482-

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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-CE4 / (2R)-2-[(R)-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro -2H-1,3-thiazine-4-carboxylic acid / cefotaxime, hydrolyzed, C3'-cleaved, open, unbound form


Mass: 413.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O6S2 / Comment: antibiotic*YM
#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.: 255 / 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: 41.05 %
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: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.74 Å / Num. all: 45653 / Num. obs: 45653 / % possible obs: 98.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.053 / Rrim(I) all: 0.138 / Rsym value: 0.127 / Net I/σ(I): 9.1 / Num. measured all: 296636
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.45-1.535.30.6843363563350.3370.0180.0470.0432.395.6
4.59-45.746.40.0431043516280.9980.0240.0620.05824.899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.6 Å40.89 Å
Translation5.6 Å40.89 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALA3.3.22data scaling
PHASER2.7.16phasing
iMOSFLM7.2.1data reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→40.894 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 4269 4.96 %Random
Rwork0.1689 81749 --
obs0.171 86018 97.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.92 Å2 / Biso mean: 17.4732 Å2 / Biso min: 6.11 Å2
Refinement stepCycle: final / Resolution: 1.45→40.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 60 255 2327
Biso mean--28.26 30.83 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052201
X-RAY DIFFRACTIONf_angle_d0.8293009
X-RAY DIFFRACTIONf_chiral_restr0.072332
X-RAY DIFFRACTIONf_plane_restr0.006400
X-RAY DIFFRACTIONf_dihedral_angle_d8.3281198
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 (%)
1.45-1.46650.32571040.31892403250785
1.4665-1.48370.34031360.32282504264090
1.4837-1.50180.3661180.31512664278294
1.5018-1.52080.38911230.30132671279495
1.5208-1.54090.30461020.29962723282595
1.5409-1.5620.36061540.28382622277696
1.562-1.58430.29731570.2812674283196
1.5843-1.60790.31131350.26322661279696
1.6079-1.63310.3211460.25222713285996
1.6331-1.65980.31091290.24282675280496
1.6598-1.68850.28621460.23512683282997
1.6885-1.71920.27531630.21942725288897
1.7192-1.75220.2521360.21262693282997
1.7522-1.7880.23561230.19372781290498
1.788-1.82690.24261180.19162769288798
1.8269-1.86940.23381820.16882744292699
1.8694-1.91610.22221540.1582723287799
1.9161-1.96790.18951560.15032802295899
1.9679-2.02580.19851420.142327912933100
2.0258-2.09120.2121440.133527692913100
2.0912-2.16590.19351820.130927672949100
2.1659-2.25270.18181330.125828202953100
2.2527-2.35520.1971400.135328012941100
2.3552-2.47930.18341620.13327882950100
2.4793-2.63460.19071390.130728032942100
2.6346-2.8380.20221570.140127952952100
2.838-3.12350.14711550.140427942949100
3.1235-3.57530.17281400.13227932933100
3.5753-4.50360.15911550.121827882943100
4.5036-40.91020.16981380.159628102948100

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