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- PDB-7e9a: Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-d... -

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Basic information

Entry
Database: PDB / ID: 7e9a
TitleCrystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S))
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / Serine-beta-lactamase KPC-2 / KPC-2 / Carbapenemase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
ACETIC ACID / Chem-J00 / DI(HYDROXYETHYL)ETHER / beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLi, G.-B. / Yan, Y.-H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291 China
National Natural Science Foundation of China (NSFC)81502989 China
National Natural Science Foundation of China (NSFC)82073698 China
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: Design and enantioselective synthesis of 3-( alpha-acrylic acid) benzoxaboroles to combat carbapenemase resistance.
Authors: Xiao, Y.C. / Chen, X.P. / Deng, J. / Yan, Y.H. / Zhu, K.R. / Li, G. / Yu, J.L. / Brem, J. / Chen, F. / Schofield, C.J. / Li, G.B.
History
DepositionMar 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation_author / database_2
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,92827
Polymers112,3184
Non-polymers2,61023
Water6,630368
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7267
Polymers28,0801
Non-polymers6466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8007
Polymers28,0801
Non-polymers7216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area10610 Å2
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8608
Polymers28,0801
Non-polymers7817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5425
Polymers28,0801
Non-polymers4624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-2 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.421, 165.421, 94.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase / Serine-Beta-Lactamase KPC-2


Mass: 28079.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Klebsiella pneumoniae / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93LQ9, beta-lactamase

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Non-polymers , 5 types, 391 molecules

#2: Chemical
ChemComp-J00 / 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid / (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid


Mass: 203.987 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9BO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 70988 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 30.48 Å2 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.055 / Rrim(I) all: 0.245 / Χ2: 1.059 / Net I/σ(I): 3.6 / Num. measured all: 1412966
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.25-2.2916.51.70135160.6510.431.7560.923
2.29-2.3317.21.48835420.7170.3691.5330.934
2.33-2.38201.43234960.8090.3271.470.972
2.38-2.4220.61.30835160.8240.2931.340.986
2.42-2.4820.71.0835480.8630.2421.1070.965
2.48-2.5320.70.93834800.8830.210.9620.981
2.53-2.620.40.80135150.9080.1810.8220.983
2.6-2.6720.20.69235410.9370.1570.711.004
2.67-2.7519.80.58835340.9510.1350.6031.031
2.75-2.8318.20.4935270.9530.1170.5040.984
2.83-2.9420.80.46735330.9590.1040.4781.071
2.94-3.0520.90.40835220.970.0910.4181.095
3.05-3.1920.80.30835490.9840.0690.3161.143
3.19-3.3620.80.24435460.9890.0550.2511.165
3.36-3.5720.20.19335350.990.0440.1981.189
3.57-3.8519.50.16235730.9930.0370.1661.144
3.85-4.2321.30.13935750.9950.0310.1421.098
4.23-4.8520.60.13335890.9940.030.1371.175
4.85-6.119.40.12636140.990.0290.131.074
6.1-5019.30.137370.9920.0240.1031.205

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.44 Å47.43 Å
Translation7.44 Å47.43 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN3

6jn3


Resolution: 2.25→47.43 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2004 2.95 %
Rwork0.1804 65843 -
obs0.1816 67847 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.36 Å2 / Biso mean: 34.8114 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 2.25→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7845 0 178 368 8391
Biso mean--37.58 34.25 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128171
X-RAY DIFFRACTIONf_angle_d1.24111097
X-RAY DIFFRACTIONf_chiral_restr0.0651248
X-RAY DIFFRACTIONf_plane_restr0.0071444
X-RAY DIFFRACTIONf_dihedral_angle_d16.3334816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2501-2.30640.279810.2012274256
2.3064-2.36880.28161260.2193411584
2.3688-2.43850.25181440.2191483399
2.4385-2.51720.24271450.20264858100
2.5172-2.60710.27161500.19224891100
2.6071-2.71150.23971510.18864900100
2.7115-2.83490.24421520.18694872100
2.8349-2.98430.26511480.20264925100
2.9843-3.17130.24611490.20224900100
3.1713-3.4160.2421480.19084916100
3.416-3.75970.19241520.16894929100
3.7597-4.30340.18731540.15084937100
4.3034-5.42060.16781530.14934973100
5.4206-47.430.22541510.1855505298

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