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- PDB-3rxx: KPC-2 carbapenemase in complex with 3-NPBA -

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Basic information

Entry
Database: PDB / ID: 3rxx
TitleKPC-2 carbapenemase in complex with 3-NPBA
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
3-NITROPHENYLBORONIC ACID / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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 1.3Nov 27, 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)28,1592
Polymers27,9931
Non-polymers1671
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.348, 66.558, 73.598
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-NPB / 3-NITROPHENYLBORONIC ACID


Mass: 166.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6BNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 16, 2009 / Details: mirrors
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 32186 / Num. obs: 29570 / % possible obs: 91.87 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 17.177 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.3
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.25 / Num. unique all: 2406 / % possible all: 75.7

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Processing

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

3c5a


Resolution: 1.62→27.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.482 / SU ML: 0.053 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19216 1496 5.1 %RANDOM
Rwork0.16037 ---
obs0.16201 28074 87.22 %-
all-32186 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 12 246 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222072
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9662832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11623.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09115323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5141517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2985
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3710.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.26421356
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.91832122
X-RAY DIFFRACTIONr_scbond_it3.2482816
X-RAY DIFFRACTIONr_scangle_it4.4913702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.619→1.661 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 91 -
Rwork0.258 1652 -
obs--74.71 %

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