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- PDB-6j8q: Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibito... -

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Basic information

Entry
Database: PDB / ID: 6j8q
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
ACETIC ACID / Chem-BHU / DI(HYDROXYETHYL)ETHER / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.787 Å
AuthorsLi, G.-B. / Liu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81874291; 81502989 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
DepositionJan 21, 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

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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)115,27732
Polymers112,3184
Non-polymers2,95828
Water14,556808
1
A: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,12011
Polymers28,0801
Non-polymers1,04010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10900 Å2
MethodPISA
2
B: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8018
Polymers28,0801
Non-polymers7227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10760 Å2
MethodPISA
3
C: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6256
Polymers28,0801
Non-polymers5455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area10950 Å2
MethodPISA
4
D: Serine Beta-Lactamase KPC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7317
Polymers28,0801
Non-polymers6526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.159, 165.159, 94.895
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 / Beta-lactamase


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, UniProt: Q9F663*PLUS, beta-lactamase

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Non-polymers , 5 types, 836 molecules

#2: Chemical
ChemComp-BHU / [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid / (S)-((3-mercapto-2-methylpropanamido)methyl)boronic acid


Mass: 177.030 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12BNO3S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

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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: 63.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 32% to 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: 136404 / % possible obs: 97 % / Redundancy: 16.5 % / Biso Wilson estimate: 21.49 Å2 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.057 / Rrim(I) all: 0.228 / Χ2: 0.985 / Net I/σ(I): 3.1 / Num. measured all: 2249490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.78-1.845.7116330.1190.910.74683.4
1.84-1.929.4134740.2610.6380.76796.4
1.92-213.5136590.5310.4310.80298
2-2.1116.1137600.7240.3010.8498.1
2.11-2.2418.9137610.8740.2140.90598.60.9190.944
2.24-2.4219138690.9220.1580.99598.90.6790.697
2.42-2.6619.2138790.9580.1061.18698.70.4610.473
2.66-3.0420.2139730.9770.0731.38599.30.3230.331
3.04-3.8320.4140250.9860.0470.99299.10.2090.214
3.83-5020.4143710.990.0360.82799.30.1570.161

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.4 Å47.68 Å
Translation7.4 Å47.68 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RXW

3rxw


Resolution: 1.787→47.677 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.5
RfactorNum. reflection% reflection
Rfree0.2052 1983 1.83 %
Rwork0.1704 --
obs0.171 108182 77.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.22 Å2 / Biso mean: 23.3258 Å2 / Biso min: 4.31 Å2
Refinement stepCycle: final / Resolution: 1.787→47.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7839 0 190 811 8840
Biso mean--34.03 31.5 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118165
X-RAY DIFFRACTIONf_angle_d1.15211064
X-RAY DIFFRACTIONf_chiral_restr0.0641244
X-RAY DIFFRACTIONf_plane_restr0.0071437
X-RAY DIFFRACTIONf_dihedral_angle_d16.1424824
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 (%)
1.7871-1.83180.275370.2734664735
1.8318-1.88140.3154290.26911469149815
1.8814-1.93670.3736530.25722861291429
1.9367-1.99920.31781010.25165512561356
1.9992-2.07070.28761410.23378021816281
2.0707-2.15360.25421810.20759509969097
2.1536-2.25160.23821840.18659650983499
2.2516-2.37030.2361820.17589720990299
2.3703-2.51880.19821800.16629669984999
2.5188-2.71330.17941790.15929760993999
2.7133-2.98630.23761870.16759803999099
2.9863-3.41830.1861830.16919764994799
3.4183-4.30630.16871920.142992110113100
4.3063-47.69420.18271840.1602100741025899

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