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- PDB-6jn3: Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibito... -

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Basic information

Entry
Database: PDB / ID: 6jn3
TitleSerine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05
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
ACETIC ACID / Chem-BX6 / DI(HYDROXYETHYL)ETHER / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.216 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 20, 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)114,44421
Polymers112,3184
Non-polymers2,12617
Water9,926551
1
A: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5735
Polymers28,0801
Non-polymers4934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7256
Polymers28,0801
Non-polymers6465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5735
Polymers28,0801
Non-polymers4934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5735
Polymers28,0801
Non-polymers4934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.515, 165.515, 94.681
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: 28079.584 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-BX6 / [(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid


Mass: 267.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18BNO3S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
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: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 192362 / % possible obs: 96.7 % / Redundancy: 17.4 % / Biso Wilson estimate: 21.02 Å2 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.059 / Rrim(I) all: 0.231 / Χ2: 1.007 / Net I/σ(I): 3.4 / Num. measured all: 2388937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.78-1.815.845310.1640.780.93664.5
1.81-1.847.255650.2080.6940.9679.4
1.84-1.888.564870.2370.6370.97491.8
1.88-1.9210.469430.390.5610.97698.6
1.92-1.9612.570230.5740.4590.97899.8
1.96-214.970720.7230.3791.002100
2-2.051670390.830.3141.001100
2.05-2.111970850.8760.2731.005100
2.11-2.1720.970200.9040.2171.0081000.9680.993
2.17-2.242170820.9250.1831.0021000.8160.836
2.24-2.3220.670740.930.1551.0121000.6880.705
2.32-2.4220.370550.9550.1270.9951000.5590.574
2.42-2.5318.970620.9660.1010.9971000.4320.444
2.53-2.6621.270980.9740.0791.0141000.3550.364
2.66-2.8321.171020.9780.0661.0141000.2930.3
2.83-3.0420.971130.9840.0560.9921000.250.257
3.04-3.3519.671270.9790.0481.0081000.2080.214
3.35-3.8321.571390.9850.0411.0241000.1860.19
3.83-4.8319.971960.9860.041.0031000.1740.178
4.83-5020.573920.9710.041.0851000.1760.18

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.42 Å47.78 Å
Translation7.42 Å47.78 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5eec

5eec


Resolution: 2.216→47.78 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.15
RfactorNum. reflection% reflection
Rfree0.2011 2637 1.84 %
Rwork0.1668 --
obs0.1675 143166 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.21 Å2 / Biso mean: 25.1732 Å2 / Biso min: 3.78 Å2
Refinement stepCycle: final / Resolution: 2.216→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7854 0 142 554 8550
Biso mean--38.05 29.8 -
Num. residues----1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128158
X-RAY DIFFRACTIONf_angle_d1.24111085
X-RAY DIFFRACTIONf_chiral_restr0.0611252
X-RAY DIFFRACTIONf_plane_restr0.0081447
X-RAY DIFFRACTIONf_dihedral_angle_d16.3564810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2161-2.25640.23271310.20766839697092
2.2564-2.29980.25061250.2037231735696
2.2998-2.34670.22931390.19174037542100
2.3467-2.39770.25271420.188474787620100
2.3977-2.45350.27081440.183173727516100
2.4535-2.51480.24831420.174374977639100
2.5148-2.58280.20051360.163174387574100
2.5828-2.65880.19541340.159173417475100
2.6588-2.74460.23991440.1675117655100
2.7446-2.84270.20541380.160674657603100
2.8427-2.95650.20411400.168574267566100
2.9565-3.09110.21831340.179374467580100
3.0911-3.2540.19341460.172374627608100
3.254-3.45780.20861380.170574587596100
3.4578-3.72470.18361400.159574077547100
3.7247-4.09940.19221420.15274417583100
4.0994-4.69210.17461400.141174587598100
4.6921-5.90980.16321460.156274617607100
5.9098-47.79120.16841360.17487395753199

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