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- PDB-9fqx: Pseudomonas aeruginosa Elastase in complex with a phosphonate bas... -

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Basic information

Entry
Database: PDB / ID: 9fqx
TitlePseudomonas aeruginosa Elastase in complex with a phosphonate based inhibitor (S-configured)
ComponentsElastase
KeywordsHYDROLASE / Virulence factor / 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 ...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: 1.8 Å
AuthorsKlein, A. / Hirsch, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: To Be Published
Title: Pseudomonas aeruginosa Elastase in complex with S-configured phosphonate based inhibitor
Authors: Klein, A. / Hirsch, A.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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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)33,7694
Polymers33,1761
Non-polymers5943
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area11990 Å2
Unit cell
Length a, b, c (Å)40.594, 89.839, 41.290
Angle α, β, γ (deg.)90.000, 114.425, 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

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


Mass: 33175.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: P14756, 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-A1IJJ / [(2~{S})-1-[[(2~{S})-1-[(3,4-dichlorophenyl)amino]-1-oxidanylidene-3-pyridin-2-yl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]phosphonic acid


Mass: 488.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24Cl2N3O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium chloride, 20.0% (w/v) PEG 3350

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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: Aug 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.8→44.92 Å / Num. obs: 24776 / % possible obs: 99.15 % / Redundancy: 2 % / Biso Wilson estimate: 18.02 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.62
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 2481 / CC1/2: 0.959

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot1.19.2_4158model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.92 Å / SU ML: 0.1667 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1666 1271 5.13 %
Rwork0.1441 23504 -
obs0.1453 24775 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 33 236 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052411
X-RAY DIFFRACTIONf_angle_d0.76923269
X-RAY DIFFRACTIONf_chiral_restr0.0462326
X-RAY DIFFRACTIONf_plane_restr0.0093433
X-RAY DIFFRACTIONf_dihedral_angle_d11.9202339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.25421440.18582595X-RAY DIFFRACTION99.38
1.87-1.960.18761280.15022621X-RAY DIFFRACTION98.96
1.96-2.060.2013980.13682614X-RAY DIFFRACTION97.98
2.06-2.190.1911130.13952647X-RAY DIFFRACTION99.93
2.19-2.360.16561130.12912642X-RAY DIFFRACTION99.67
2.36-2.60.17371300.13612637X-RAY DIFFRACTION99.53
2.6-2.970.16462130.14462515X-RAY DIFFRACTION98.27
2.97-3.740.14811790.13482602X-RAY DIFFRACTION99.75
3.74-44.920.15471530.15452631X-RAY DIFFRACTION98.9
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)
11.807726295320.117658340896-0.1165731935932.598790946150.1331872553852.926456418530.0215896751271-0.09646021261890.3962371507330.2302764092850.08071787611050.141210123264-0.194185660102-0.109288526575-0.08060621344330.130487880880.03224859616450.003082637618690.108112591581-0.002511536434590.200842545598-15.39183813196.75788588409-19.805178798
20.864177945788-0.0223965854619-0.08820873025762.24005745101-2.146323705174.50231393943-0.0193978219343-0.1249869252460.1952601207120.1242717793860.0660012265809-0.011568836744-0.201126077823-0.0485819094134-0.03848141257380.09368504902620.01686741691350.006583748553990.10897185295-0.04982843071290.168838732818-9.187550462142.42389271-16.1652058365
30.1184521966890.5757479747230.4651570271522.635313418681.64594252167.928636167940.0869015158772-0.1051200615960.1351006276090.1197244611580.208464654271-0.40779937662-0.04556842592140.531613713847-0.2917557309480.1354165415830.0230395614832-0.03827810059790.222635834459-0.04878149036260.286392540505-0.084648964553.79265185814-22.8919103701
41.28933774236-0.2294061694110.1022975854370.9951406622770.2900935944210.9102074161-0.0280230732309-0.0510818206206-0.03016083556950.0816237272433-0.01831415848670.06051366063440.0588769275354-0.02838748101820.04991806353920.1326506640880.00100874010004-0.001814337452710.104064952973-0.01792463144670.09133191026783.65013723692-14.3420655738-11.1340837877
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 61 )1 - 611 - 61
22chain 'A' and (resid 62 through 109 )62 - 10962 - 109
33chain 'A' and (resid 110 through 134 )110 - 134110 - 134
44chain 'A' and (resid 135 through 298 )135 - 298135 - 298

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