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- PDB-6jn4: Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibito... -

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Basic information

Entry
Database: PDB / ID: 6jn4
TitleSerine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001
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
ACETATE ION / ACETIC ACID / Chem-BX9 / 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: 1.9 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 6, 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: 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)114,78825
Polymers112,3184
Non-polymers2,47021
Water11,836657
1
A: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7427
Polymers28,0801
Non-polymers6636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8948
Polymers28,0801
Non-polymers8157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6826
Polymers28,0801
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4704
Polymers28,0801
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.785, 164.785, 94.683
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
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

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Non-polymers , 5 types, 678 molecules

#2: Chemical
ChemComp-BX9 / [(R)-(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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
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: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 116149 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 19.14 Å2 / Rmerge(I) obs: 0.305 / Rpim(I) all: 0.071 / Rrim(I) all: 0.313 / Χ2: 0.979 / Net I/σ(I): 3.9 / Num. measured all: 2274445
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.9-1.9319.557710.7270.280.834100
1.93-1.9719.657530.7910.240.857100
1.97-2.0119.457680.8410.2080.881000.9060.93
2.01-2.0519.357470.8640.1810.8841000.7810.802
2.05-2.0919.158060.8860.1620.9071000.6940.713
2.09-2.1418.757600.8990.1450.9091000.6170.634
2.14-2.1917.257650.9070.1320.9341000.5360.552
2.19-2.2519.857770.9330.1160.9421000.5080.521
2.25-2.3220.157850.9360.1060.971000.4690.481
2.32-2.392057620.950.0980.9821000.4320.443
2.39-2.482057730.9540.0911.0111000.3970.408
2.48-2.582058000.9550.0831.0361000.3650.374
2.58-2.719.658070.9610.0791.0451000.3430.352
2.7-2.8417.958060.9590.0781.0591000.3240.334
2.84-3.0220.757930.9670.0711.0721000.3170.325
3.02-3.2520.858430.9710.0681.0891000.3020.309
3.25-3.5820.658350.9670.0661.0941000.2910.298
3.58-4.0919.158500.960.0661.0741000.2820.289
4.09-5.1620.658940.9710.0611.0061000.2730.279
5.16-5019.860540.9680.0610.9699.70.2690.276

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.96 Å47.57 Å
Translation6.96 Å47.57 Å

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Processing

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

5lca


Resolution: 1.9→47.569 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.221 1990 1.73 %
Rwork0.1805 --
obs0.1812 115321 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.87 Å2 / Biso mean: 22.5656 Å2 / Biso min: 1.42 Å2
Refinement stepCycle: final / Resolution: 1.9→47.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7828 0 164 660 8652
Biso mean--28.86 26.22 -
Num. residues----1051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128142
X-RAY DIFFRACTIONf_angle_d1.14211059
X-RAY DIFFRACTIONf_chiral_restr0.0611249
X-RAY DIFFRACTIONf_plane_restr0.0071441
X-RAY DIFFRACTIONf_dihedral_angle_d15.8514785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9003-1.94780.29061380.24497723786196
1.9478-2.00050.2621420.22317988813099
2.0005-2.05930.25051380.21298056819499
2.0593-2.12580.25371440.201380498193100
2.1258-2.20180.27121420.20298084822699
2.2018-2.28990.23151420.190880828224100
2.2899-2.39410.23591420.184580968238100
2.3941-2.52040.2441430.175580978240100
2.5204-2.67830.20791480.169781088256100
2.6783-2.8850.19811440.174781738317100
2.885-3.17530.25661440.185481528296100
3.1753-3.63460.18691420.172881438285100
3.6346-4.57870.20581330.15682228355100
4.5787-47.58420.18511480.16928358850699

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