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- PDB-6f8b: LasB bound to thiol based inhibitor -

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Basic information

Entry
Database: PDB / ID: 6f8b
TitleLasB bound to thiol based inhibitor
ComponentsElastase
KeywordsHYDROLASE / LasB / inhibitor
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 / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / 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 ...Elastase; domain 1 - #10 / Elastase; domain 1 / 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 / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
~{N}-(3,4-dichlorophenyl)-2-sulfanyl-ethanamide / Neutral metalloproteinase / Elastase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKO4116/31 Germany
CitationJournal: ACS Infect Dis / Year: 2018
Title: Binding Mode Characterization and Early in Vivo Evaluation of Fragment-Like Thiols as Inhibitors of the Virulence Factor LasB from Pseudomonas aeruginosa.
Authors: Kany, A.M. / Sikandar, A. / Haupenthal, J. / Yahiaoui, S. / Maurer, C.K. / Proschak, E. / Kohnke, J. / Hartmann, R.W.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: Elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7535
Polymers33,1761
Non-polymers5784
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.293, 89.998, 41.857
Angle α, β, γ (deg.)90.00, 114.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Elastase /


Mass: 33175.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Pseudomonas aeruginosa (bacteria)
References: UniProt: I6R951, UniProt: P14756*PLUS, pseudolysin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CXH / ~{N}-(3,4-dichlorophenyl)-2-sulfanyl-ethanamide


Mass: 236.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7Cl2NOS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 0.2 M Magnesium chloride, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.3→38.22 Å / Num. obs: 64739 / % possible obs: 96.96 % / Redundancy: 2 % / Rmerge(I) obs: 0.02876 / Net I/σ(I): 17.78
Reflection shellResolution: 1.3→1.346 Å / Rmerge(I) obs: 0.1924

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZM

1ezm


Resolution: 1.3→44.999 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 3121 4.82 %
Rwork0.1427 --
obs0.1435 64720 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→44.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 28 414 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082375
X-RAY DIFFRACTIONf_angle_d0.9753226
X-RAY DIFFRACTIONf_dihedral_angle_d15.648816
X-RAY DIFFRACTIONf_chiral_restr0.087324
X-RAY DIFFRACTIONf_plane_restr0.007429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32030.24531350.20332714X-RAY DIFFRACTION94
1.3203-1.3420.21911460.19842705X-RAY DIFFRACTION95
1.342-1.36510.20031260.18242712X-RAY DIFFRACTION95
1.3651-1.38990.22291420.18212775X-RAY DIFFRACTION95
1.3899-1.41670.18491020.17722753X-RAY DIFFRACTION95
1.4167-1.44560.17711000.16582828X-RAY DIFFRACTION95
1.4456-1.4770.18921180.15782762X-RAY DIFFRACTION96
1.477-1.51140.16351250.15582784X-RAY DIFFRACTION96
1.5114-1.54920.15991170.14242863X-RAY DIFFRACTION97
1.5492-1.59110.16181630.14112704X-RAY DIFFRACTION96
1.5911-1.63790.15971500.142778X-RAY DIFFRACTION96
1.6379-1.69080.1361300.13512799X-RAY DIFFRACTION97
1.6908-1.75120.15361200.13982842X-RAY DIFFRACTION97
1.7512-1.82130.17691380.14192800X-RAY DIFFRACTION97
1.8213-1.90420.15031510.13762817X-RAY DIFFRACTION98
1.9042-2.00460.1731600.13582824X-RAY DIFFRACTION98
2.0046-2.13020.13791680.12922827X-RAY DIFFRACTION99
2.1302-2.29460.12921990.12142774X-RAY DIFFRACTION99
2.2946-2.52550.1371370.12962897X-RAY DIFFRACTION99
2.5255-2.89090.15691890.13532827X-RAY DIFFRACTION99
2.8909-3.6420.16641620.13392875X-RAY DIFFRACTION99
3.642-45.0260.14841430.14592939X-RAY DIFFRACTION100
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)
10.0202-0.03710.03760.1252-0.11910.10140.02370.03330.0619-0.12170.13190.21220.0755-0.08460.04360.0646-0.0136-0.01340.07830.02990.1247-16.13847.9622-26.8128
20.09760.0718-0.0670.0683-0.09340.1293-0.00740.02540.19460.09570.15070.2856-0.0597-0.10680.01610.11510.03250.05120.08540.01070.1715-17.193115.9251-16.3368
30.0103-0.00110.06520.07220.16141.06750.0116-0.01670.07730.14310.13390.1971-0.46340.18410.12660.10730.07690.0131-0.01010.04710.2209-11.151524.0376-21.3856
40.2068-0.04310.02750.1302-0.06390.0977-0.0112-0.05390.08630.00640.03940.0769-0.03620.0018-0.00660.07690.00150.00670.0626-0.00460.0573-8.443712.4036-17.619
50.0175-0.0042-0.01570.061-0.03910.02570.0193-0.01410.040.01440.0158-0.03290.04670.0591-0.00020.0985-0.0086-0.00840.0733-0.00970.0721-0.482213.5169-23.1748
60.0110.0162-0.00420.0437-0.0180.0243-0.0801-0.0220.09330.01210.009-0.0116-0.0975-0.0102-0.00060.07310.0048-0.00550.078-0.00770.07483.49626.5684-9.2031
70.01340.01990.00160.13680.01990.0190.0026-0.02420.08060.0279-0.01370.03020.0107-0.009300.05260.00090.00250.06790.0050.0707-0.5047-0.2286-13.3687
80.0195-0.03180.01440.05290.02060.04110.0025-0.0003-0.0613-0.0707-0.07350.0331-0.00750.0471-0.00560.08660.0097-0.00190.07690.00760.0575-1.2209-0.9734-25.8427
90.3415-0.12170.15270.30260.01290.17590.0031-0.039-0.02180.02030.0151-0.01530.0459-0.021600.0559-0.00430.00080.06480.01190.04815.8285-6.5619-10.4558
100.13260.09960.04980.09340.040.018-0.0236-0.0483-0.23740.09170.0864-0.02550.161-0.01660.02920.0967-0.0114-0.0010.09770.05150.09043.9895-15.0665-5.3184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 199 )
9X-RAY DIFFRACTION9chain 'A' and (resid 200 through 278 )
10X-RAY DIFFRACTION10chain 'A' and (resid 279 through 298 )

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