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- PDB-7ti2: Structure of KPC-2 bound to RPX-7063 at 1.75A -

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Basic information

Entry
Database: PDB / ID: 7ti2
TitleStructure of KPC-2 bound to RPX-7063 at 1.75A
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / KPC-2
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/transpeptidase-like
Similarity search - Domain/homology
Chem-ZXQ / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsClifton, M.C. / Fairman, J.W. / Edwards, T.E. / Hecker, S.J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Broad-spectrum cyclic boronate beta-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability.
Authors: Raja Reddy, K. / Totrov, M. / Lomovskaya, O. / Griffith, D.C. / Tarazi, Z. / Clifton, M.C. / Hecker, S.J.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,9984
Polymers29,5651
Non-polymers4333
Water5,603311
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.100, 80.100, 44.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 29565.199 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) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-ZXQ / {(3R,7S)-2-hydroxy-3-[2-(thiophen-2-yl)acetamido]-2,3,4,7-tetrahydro-1,2-oxaborepin-7-yl}acetic acid


Mass: 309.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16BNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 26.8 mg/ml KPC-2 R4327, 2M NaCl, 100mM Bicine pH9; co-crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 6, 2012 / Details: Rigaku VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 28464 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.63 % / Biso Wilson estimate: 20.677 Å2 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Net I/σ(I): 21.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.75-1.82.630.2543.6120800.31997.2
1.8-1.842.90.2374.1620700.29399.9
1.84-1.92.970.2234.9919730.27398
1.9-1.962.830.2056.6218130.25592.3
1.96-2.023.280.1347.8218620.16199.9
2.02-2.092.980.12510.6517240.15494.2
2.09-2.173.840.09712.7617810.11399.7
2.17-2.263.960.08716.9916470.10296.9
2.26-2.364.680.08118.3816560.09298.9
2.36-2.485.180.06721.315240.074100
2.48-2.615.50.0562515040.06299.9
2.61-2.775.660.0627.4714070.06699.8
2.77-2.967.20.04930.713350.053100
2.96-3.27.430.04236.0312460.045100
3.2-3.57.030.03844.6411360.04199.9
3.5-3.916.490.03551.4410300.03899.2
3.91-4.527.120.02759.389190.0399.8
4.52-5.537.390.02558.547850.027100
5.53-7.837.30.02952.186130.031100
7.83-506.820.02365.183590.02598.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev 2050refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ov5

2ov5


Resolution: 1.75→40.05 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1487 5.23 %0
Rwork0.1572 26944 --
obs0.1584 28431 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.24 Å2 / Biso mean: 16.9845 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 29 311 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052023
X-RAY DIFFRACTIONf_angle_d1.0072756
X-RAY DIFFRACTIONf_chiral_restr0.041312
X-RAY DIFFRACTIONf_plane_restr0.005360
X-RAY DIFFRACTIONf_dihedral_angle_d12.2381191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.19251520.17022399X-RAY DIFFRACTION98
1.8065-1.87110.19271620.1682441X-RAY DIFFRACTION100
1.8711-1.9460.22111140.2012318X-RAY DIFFRACTION93
1.946-2.03450.1871490.15912459X-RAY DIFFRACTION100
2.0345-2.14180.24911250.18362349X-RAY DIFFRACTION96
2.1418-2.2760.19871270.17862422X-RAY DIFFRACTION97
2.276-2.45170.17191070.1552503X-RAY DIFFRACTION100
2.4517-2.69840.17191270.14872495X-RAY DIFFRACTION100
2.6984-3.08870.18981280.16282505X-RAY DIFFRACTION100
3.0887-3.89090.14981600.1372474X-RAY DIFFRACTION100
3.8909-400.15491360.13962579X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.88520.9130.80871.4540.07021.9218-0.20030.1120.2256-0.09420.1337-0.35370.01240.2848-0.05710.09730.0301-0.02120.1957-0.07030.265439.432814.13591.6493
21.95330.2871-0.41670.98770.46781.63870.03540.15520.0965-0.0343-0.0267-0.1237-0.0572-0.0613-0.02640.0758-0.0075-0.00330.03650.02570.099224.162620.95612.7034
32.3665-0.5666-0.67541.20910.12220.7109-0.0287-0.0098-0.17580.0528-0.07210.19220.0388-0.03410.09880.0625-0.00580.01510.0753-0.01560.08295.4512.98267.6547
41.2307-0.18350.12721.31840.25890.8309-0.0472-0.0180.10190.05880.051-0.0764-0.06680.03380.01720.0725-0.0018-0.01010.05880.00080.063320.819119.69124.7774
51.5121-0.09570.0471.1618-0.74561.0461-0.05360.0499-0.03620.04960.0641-0.21440.10440.0978-0.04650.09560.0202-0.01610.0938-0.02330.088128.556511.53072.7738
63.70651.62781.23212.26780.90710.75080.1637-0.113-0.20180.2572-0.006-0.35780.12660.0929-0.14450.08740.0005-0.03490.1195-0.01390.178638.68289.35118.1743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 31 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 106 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 204 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 249 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 267 )A0

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