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- PDB-3rxw: KPC-2 carbapenemase in complex with PSR3-226 -

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Basic information

Entry
Database: PDB / ID: 3rxw
TitleKPC-2 carbapenemase in complex with PSR3-226
ComponentsCarbepenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / beta-lactamase / 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
CITRIC ACID / Chem-SR3 / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsKe, W. / van den Akker, F.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2012
Title: Crystal structures of KPC-2 {beta}-lactamase in complex with 3-nitrophenyl boronic acid and the penam sulfone PSR-3-226.
Authors: Ke, W. / Bethel, C.R. / Papp-Wallace, K.M. / Pagadala, S.R. / Nottingham, M. / Fernandez, D. / Buynak, J.D. / Bonomo, R.A. / van den Akker, F.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5093
Polymers27,9931
Non-polymers5162
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.051, 66.288, 71.776
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 Carbepenem-hydrolyzing beta-lactamase KPC / KPC-1 / KPC-2


Mass: 27992.506 Da / Num. of mol.: 1 / Fragment: UNP residues 26-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, BLAKPC-2, kpc, kpc1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-SR3 / (2S,3R)-4-(2-amino-2-oxoethoxy)-3-(dihydroxy-lambda~4~-sulfanyl)-3-methyl-4-oxo-2-{[(1E)-3-oxoprop-1-en-1-yl]amino}butanoic acid


Mass: 324.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG6000, 100 mM potassium thiocyanate, 100 mM citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.984
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2009 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. all: 63842 / Num. obs: 62504 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.07
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.4 / % possible all: 82.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C5A

3c5a


Resolution: 1.26→33.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.565 / SU ML: 0.025 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17139 3182 5.1 %RANDOM
Rwork0.15588 ---
obs0.15666 59322 97.9 %-
all-63842 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.26→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 34 316 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222109
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9782887
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06823.64785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79815320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.681515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211631
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21052
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21493
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4161.51339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42222142
X-RAY DIFFRACTIONr_scbond_it3.9453770
X-RAY DIFFRACTIONr_scangle_it6.4634.5737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 194 -
Rwork0.231 3513 -
obs--79.94 %

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