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- PDB-6jn5: Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibito... -

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Basic information

Entry
Database: PDB / ID: 6jn5
TitleSerine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23
ComponentsSerine Beta-Lactamase KPC-2
KeywordsHYDROLASE / Beta-lactamase / Serine-beta-lactamase KPC-2 / KPC-2 / Carbapenemase
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-BXU / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsLi, G.-B. / Liu, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81874291 China
National Natural Science Foundation of China81502989 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases.
Authors: Wang, Y.L. / Liu, S. / Yu, Z.J. / Lei, Y. / Huang, M.Y. / Yan, Y.H. / Ma, Q. / Zheng, Y. / Deng, H. / Sun, Y. / Wu, C. / Yu, Y. / Chen, Q. / Wang, Z. / Wu, Y. / Li, G.B.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine Beta-Lactamase KPC-2
B: Serine Beta-Lactamase KPC-2
C: Serine Beta-Lactamase KPC-2
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0548
Polymers111,9704
Non-polymers1,0844
Water3,783210
1
A: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2642
Polymers27,9931
Non-polymers2711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2642
Polymers27,9931
Non-polymers2711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2642
Polymers27,9931
Non-polymers2711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2642
Polymers27,9931
Non-polymers2711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.757, 164.757, 94.499
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
Serine Beta-Lactamase KPC-2


Mass: 27992.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPC-2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase
#2: Chemical
ChemComp-BXU / [(S)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid


Mass: 271.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15BFNO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35% (v/v) Polyethylene glycol 8000

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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: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 158548 / % possible obs: 98.6 % / Redundancy: 17 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.355 / Rpim(I) all: 0.094 / Rrim(I) all: 0.366 / Χ2: 0.93 / Net I/σ(I): 2.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.7-1.768.3138730.2420.530.72986.8
1.76-1.8311.1158830.3920.4930.73899.6
1.83-1.9116.3160030.6440.3830.766100
1.91-2.0219.2159590.8340.2690.816100
2.02-2.1419.3160030.8830.1970.8821000.8460.869
2.14-2.3119.4160480.9090.1470.9691000.6340.651
2.31-2.5420.2160230.9270.1191.071000.5160.53
2.54-2.9118.9160810.9420.11.1371000.4220.434
2.91-3.6619.2161700.9610.0821.0871000.3420.352
3.66-5016.9165050.9680.0720.8481000.2820.291

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å47.56 Å
Translation1.7 Å47.56 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEC

5eec


Resolution: 1.97→47.561 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.11
RfactorNum. reflection% reflection
Rfree0.3164 1681 1.64 %
Rwork0.2745 --
obs0.2752 102537 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.96 Å2 / Biso mean: 17.5114 Å2 / Biso min: 0.79 Å2
Refinement stepCycle: final / Resolution: 1.97→47.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7819 0 72 210 8101
Biso mean--28.34 12.91 -
Num. residues----1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158055
X-RAY DIFFRACTIONf_angle_d1.32610974
X-RAY DIFFRACTIONf_chiral_restr0.0661244
X-RAY DIFFRACTIONf_plane_restr0.0091431
X-RAY DIFFRACTIONf_dihedral_angle_d16.5664756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.0280.35021260.28897590771690
2.028-2.09350.35841360.29448309844598
2.0935-2.16830.37921430.29758423856699
2.1683-2.25510.40141390.29028435857499
2.2551-2.35770.35851390.28284578596100
2.3577-2.4820.36871400.277984678607100
2.482-2.63750.31511410.2718458859999
2.6375-2.84110.31141390.27438478861799
2.8411-3.1270.29781440.279185048648100
3.127-3.57940.29921410.26568535867699
3.5794-4.50910.27061460.25338556870299
4.5091-47.57510.27631470.27258644879198

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