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- PDB-7z68: Pseudomonas aeruginosa Elastase in complex with a Thiol based inh... -

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Basic information

Entry
Database: PDB / ID: 7z68
TitlePseudomonas aeruginosa Elastase in complex with a Thiol based inhibitor (R-and S-configured)
ComponentsKeratinase KP2
KeywordsHYDROLASE / Virulence factor / Inhibitor / Complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase 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
Similarity search - Domain/homology
Chem-IEV / Neutral metalloproteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKlein, A. / Hirsch, A.
Funding support Germany, European Union, 4items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Helmholtz Association Germany
European Research Council (ERC)716311European Union
European Research Council (ERC)757913European Union
CitationJournal: To Be Published
Title: Dual inhibitors of Pseudomonas aeruginosa virulence factors LecA and LasB
Authors: Klein, A. / Hirsch, A.
History
DepositionMar 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8255
Polymers33,1761
Non-polymers6494
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-16 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.316, 92.527, 40.745
Angle α, β, γ (deg.)90.000, 114.227, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Keratinase KP2


Mass: 33175.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria)
References: UniProt: E3ULB4, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 301 molecules

#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-IEV / (2~{R})-~{N}-[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanylphenyl]-3-phenyl-2-sulfanyl-propanamide


Mass: 451.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25NO6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: Potassium nitrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→92.53 Å / Num. obs: 42420 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.348 / Num. unique obs: 2067 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FZX

6fzx


Resolution: 1.5→37.16 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 2022 4.77 %
Rwork0.1566 40359 -
obs0.1583 42381 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.33 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 38 297 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152448
X-RAY DIFFRACTIONf_angle_d1.37033317
X-RAY DIFFRACTIONf_chiral_restr0.0677336
X-RAY DIFFRACTIONf_plane_restr0.0127435
X-RAY DIFFRACTIONf_dihedral_angle_d17.7515344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.26751750.2062793X-RAY DIFFRACTION99.4
1.54-1.580.26741660.18952860X-RAY DIFFRACTION99.97
1.58-1.630.2141860.18072859X-RAY DIFFRACTION99.93
1.63-1.680.20661560.17292857X-RAY DIFFRACTION100
1.68-1.740.18731500.17242869X-RAY DIFFRACTION99.97
1.74-1.810.21421500.16192869X-RAY DIFFRACTION99.97
1.81-1.890.22371590.15652878X-RAY DIFFRACTION100
1.89-1.990.20841290.1532879X-RAY DIFFRACTION99.93
1.99-2.110.17841200.15342888X-RAY DIFFRACTION99.67
2.11-2.280.16441220.14462924X-RAY DIFFRACTION99.97
2.28-2.510.1841110.14742925X-RAY DIFFRACTION100
2.51-2.870.18821430.14812894X-RAY DIFFRACTION99.97
2.87-3.610.1757940.15062955X-RAY DIFFRACTION99.84
3.61-37.160.1921610.15792909X-RAY DIFFRACTION99.74
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)
13.609586571091.727653866630.2620764927743.929490008990.1042037607662.06511057908-0.104742938433-0.0772108185176-0.04141357984250.0877010903180.04552753010620.299290783970.155840646656-0.1943323566370.0472354993210.119324183881-0.004121771027510.003415757776280.0989291148610.02013951437130.0959126004194-2.44544316809-4.070836957866.31749571124
24.70995001622-0.924394062555-0.7825528984833.543314242960.6657751499612.7644934322-0.1681224228940.43639439386-0.28618515085-0.3386187792080.1736735613730.0117247994910.389300652715-0.235067103785-0.006457539740510.325635916964-0.06171855973370.03960980368160.122601237416-0.002693035631850.198544349920.442811821832-15.3082618308-0.0230835301858
30.762538437211-0.4776435672740.7245006744181.37045474903-0.9536162142181.686280569430.0188207480380.0747892512138-0.0706080544991-0.1830420514140.02537873080230.05948359520570.248055653228-0.0404996274858-0.05250148728130.15005487753-0.0304804038818-0.001152661920270.103170482136-0.009354195516450.1039571388360.155983689042-2.16928779663-7.23244138817
40.9625862918840.118891528379-0.3329245934991.21106130235-0.2576821271591.729084761430.03639436522140.01724028717150.10157476978-0.04978876632420.003062754366670.0681632017826-0.0535202057037-0.0456145190528-0.03119086315960.0725830411957-0.0008425877846650.0002101196169330.06579506171860.003773668808180.09186729614070.032552049521615.1617554508-16.018607436
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 40 )1 - 401 - 40
22chain 'A' and (resid 41 through 60 )41 - 6041 - 60
33chain 'A' and (resid 61 through 156 )61 - 15661 - 156
44chain 'A' and (resid 157 through 298 )157 - 298157 - 298

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