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- PDB-8cc4: LasB bound to phosphonic acid based inhibitor -

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Basic information

Entry
Database: PDB / ID: 8cc4
TitleLasB bound to phosphonic acid based inhibitor
ComponentsElastase
KeywordsHYDROLASE / LasB / (4-methyl-1-oxo-1-((4-(trifluoromethyl)phenyl)amino)pentan-2-yl)phosphonic acid inhibitor complex
Function / homology
Function and homology information


pseudolysin / protein transport by the Sec complex / protein secretion by the type II secretion system / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / metalloendopeptidase activity / endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMueller, R. / Sikandar, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: Inhibitors of the Elastase LasB for the Treatment of Pseudomonas aeruginosa Lung Infections.
Authors: Konstantinovic, J. / Kany, A.M. / Alhayek, A. / Abdelsamie, A.S. / Sikandar, A. / Voos, K. / Yao, Y. / Andreas, A. / Shafiei, R. / Loretz, B. / Schonauer, E. / Bals, R. / Brandstetter, H. / ...Authors: Konstantinovic, J. / Kany, A.M. / Alhayek, A. / Abdelsamie, A.S. / Sikandar, A. / Voos, K. / Yao, Y. / Andreas, A. / Shafiei, R. / Loretz, B. / Schonauer, E. / Bals, R. / Brandstetter, H. / Hartmann, R.W. / Ducho, C. / Lehr, C.M. / Beisswenger, C. / Muller, R. / Rox, K. / Haupenthal, J. / Hirsch, A.K.H.
History
DepositionJan 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elastase
B: Elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2418
Polymers66,3512
Non-polymers8896
Water97354
1
A: Elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6204
Polymers33,1761
Non-polymers4453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6204
Polymers33,1761
Non-polymers4453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.404, 77.114, 152.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Elastase / Neutral metalloproteinase / PAE / Pseudolysin / LasB


Mass: 33175.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lasB, PA3724 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P14756, pseudolysin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-U7F / [(2~{R})-4-methyl-1-oxidanylidene-1-[[4-(trifluoromethyl)phenyl]amino]pentan-2-yl]phosphonic acid


Mass: 339.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17F3NO4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 0.1 M Tris-Cl pH 8.5, and 1.6 Ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.1→44.4 Å / Num. obs: 14190 / % possible obs: 96.4 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.075 / Net I/σ(I): 6.8
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.598 / Num. unique obs: 1888 / CC1/2: 0.864 / Rpim(I) all: 0.242

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.4 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 686 4.84 %
Rwork0.2033 --
obs0.206 14159 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 48 54 4731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074797
X-RAY DIFFRACTIONf_angle_d0.7636508
X-RAY DIFFRACTIONf_dihedral_angle_d10.458684
X-RAY DIFFRACTIONf_chiral_restr0.047649
X-RAY DIFFRACTIONf_plane_restr0.014862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.30741400.24642687X-RAY DIFFRACTION96
2.91-3.20.34371460.24292702X-RAY DIFFRACTION96
3.2-3.660.26071360.2072676X-RAY DIFFRACTION95
3.66-4.610.22761260.16912671X-RAY DIFFRACTION93
4.62-44.40.23041380.19642737X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4086-0.72960.5151.79-0.06532.0976-0.0559-0.5535-0.13330.31590.1047-0.06060.0306-0.0873-0.06770.29640.0264-0.00040.26450.0160.223916.56838.440420.0266
22.3265-0.98170.3362.34440.32032.45850.09970.02530.02830.3389-0.0346-0.04750.0976-0.0047-0.08380.2509-0.02320.010.2060.00680.25344.137513.90358.7433
31.9973-0.65310.52761.6088-0.63310.5522-0.04190.25540.2313-0.0497-0.01450.08360.08790.2384-0.02220.25970.00980.01490.24080.00930.24957.056517.5199-0.3173
42.0964-0.24220.88731.43680.12292.76810.01880.07760.2812-0.2520.0470.2524-0.3999-0.3106-0.05450.38620.0576-0.02470.32990.05170.2984-5.973224.57990.7852
51.91950.29250.66084.4405-1.37712.6832-0.43950.029-0.2091-0.56790.19710.17180.4268-0.13250.01520.3654-0.04930.04820.2775-0.14870.4033-3.514834.231329.8335
63.59270.7650.40761.8620.17622.1125-0.3661-0.4154-0.98030.24380.2227-0.10270.0762-0.05470.01480.47490.020.15590.470.1070.50375.137828.463940.097
74.3012-0.5924-0.38441.655-0.37971.9688-0.2836-0.51120.03150.16010.21120.02920.1690.1080.12830.32780.00220.0120.3219-0.02370.26149.352237.475834.3882
84.3444-0.9942-0.92321.5221-1.26371.91010.0421-0.64130.22340.14680.08050.03190.01940.3529-0.00070.36450.0298-0.03220.2354-0.10790.276221.599441.556529.6287
94.21282.72160.86425.59180.82892.22120.010.09070.99820.3651-0.14830.8-0.1433-0.02370.12290.2532-0.0009-0.02870.3299-0.02720.358416.446941.882522.0907
103.0625-0.0241-0.59741.41751.03582.8349-0.25160.13770.2058-0.18650.2267-0.0145-0.19920.27280.06980.3041-0.0242-0.00940.2846-0.0070.245416.248348.322218.6198
113.14711.26130.58864.19571.69484.35630.02620.37040.0831-0.460.2726-0.63010.07990.844-0.26630.2667-0.01410.06840.3613-0.01520.381631.289742.45116.4528
123.27591.83860.05997.30051.29692.8895-0.16171.00720.0681-1.04570.32920.0088-0.29780.6504-0.22160.4858-0.08440.04280.56480.11490.27726.505545.87898.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 134 )
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 179 )
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 257 )
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 298 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 17 )
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 61 )
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 134 )
8X-RAY DIFFRACTION8chain 'B' and (resid 135 through 156 )
9X-RAY DIFFRACTION9chain 'B' and (resid 157 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 180 through 257 )
11X-RAY DIFFRACTION11chain 'B' and (resid 258 through 279 )
12X-RAY DIFFRACTION12chain 'B' and (resid 280 through 298 )

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