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

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Basic information

Entry
Database: PDB / ID: 9fqe
TitlePseudomonas aeruginosa Elastase in complex with a phosphonate based inhibitor (R-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: 1.6 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 R-configured inhibitor
Authors: Klein, A. / Hirsch, A.
History
DepositionJun 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 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
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area11750 Å2
Unit cell
Length a, b, c (Å)39.667, 40.108, 45.252
Angle α, β, γ (deg.)100.216, 95.064, 106.407
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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-A1IEU / [(2~{R})-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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate, 20 % (w/v) PEG 3350,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→44.05 Å / Num. obs: 33193 / % possible obs: 96.59 % / Redundancy: 9.1 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.996 / Net I/σ(I): 32.88
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 3274 / CC1/2: 0.995

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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: 1.6→44.05 Å / SU ML: 0.1254 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.8958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1801 1646 4.96 %
Rwork0.1487 31547 -
obs0.1503 33193 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.84 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 33 323 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162411
X-RAY DIFFRACTIONf_angle_d1.43413269
X-RAY DIFFRACTIONf_chiral_restr0.0849326
X-RAY DIFFRACTIONf_plane_restr0.0125433
X-RAY DIFFRACTIONf_dihedral_angle_d6.8524336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.22121540.1652571X-RAY DIFFRACTION95.15
1.65-1.70.20921440.16192561X-RAY DIFFRACTION95.21
1.7-1.760.22171150.15992621X-RAY DIFFRACTION95.87
1.76-1.830.19121450.15282637X-RAY DIFFRACTION96.13
1.83-1.910.17151360.15162624X-RAY DIFFRACTION96.3
1.92-2.020.19931520.15292590X-RAY DIFFRACTION96.35
2.02-2.140.20331310.13812612X-RAY DIFFRACTION96.04
2.14-2.310.15351190.13872648X-RAY DIFFRACTION96.21
2.31-2.540.17121290.1382660X-RAY DIFFRACTION97.65
2.54-2.910.15961340.14282667X-RAY DIFFRACTION97.56
2.91-3.660.16591440.14822668X-RAY DIFFRACTION97.77
3.66-44.050.17621430.15532688X-RAY DIFFRACTION99.06
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)
11.60636870885-0.9681029880650.3818332752332.08902437611-0.6702479596862.084621077660.02894792039470.0754881834762-0.118182219779-0.0347214778993-0.0800534535974-0.07111483851220.1588573836050.08435740816860.05212585562730.06736822652420.01444521727530.006589071292330.0765385313231-0.01472551051180.0431787015893-9.50305854863-8.979062802474.73988098026
21.15146618688-0.411933636926-0.5297783989950.8357737374360.5521054477321.405561795860.01300871348710.0178913535348-0.0240696363749-0.02690340143730.00824391221585-0.03307740540170.1634314159950.233384222531-0.01919289282840.0428446585635-0.005266649503590.0009568388341640.04239251259530.003151221652140.0597776275406-10.596387761-4.370340616428.38436152756
31.34830317087-0.06287459259460.05742729266891.62633916339-1.165766228132.81067451750.01789296058860.0698396366045-0.0667795901407-0.08323360336140.03663553380560.09455207561010.137932047295-0.0995839043065-0.05744300656220.0449663572429-0.00646612048705-0.002883883045920.0415648591153-0.01618424765860.0588736037516-21.9534353364-7.304849923727.91266400224
41.05120334307-0.1968985759930.3469262797550.7825953204680.06130790250521.14215659020.02393839650440.0292319889770.0180294087228-0.0444854440227-0.0425542883015-0.0017040811612-0.04255792024670.02653316686650.01563333824490.0442224110417-0.001941011915140.001784026279750.0438211383448-0.001536161198240.0401614402271-23.56397466963.1864751814816.2200227038
54.027283599451.66150502958-1.675866705343.47682186794-0.7459994392852.725903614330.01770603986350.03893607536020.185683979746-0.106720207633-0.04248048870040.117406098255-0.0863333470119-0.1254072701120.01690838137130.04314342289970.0105098631873-0.01617191927550.0540660635380.004459793227590.0633999367759-38.022121894610.602969770217.0904254297
61.34694622187-0.1970137365890.4259703845190.8758508687740.07723637175810.98162644438-0.0622591659332-0.2108275284550.06618729898160.1150835318480.03225767191710.00539523312496-0.0356127659871-0.07828015601250.03129883264240.06295711393010.001680668196640.00077708157040.069567551252-0.007423097899660.0424591517255-25.54177496957.2925657626329.7158498386
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 56 )1 - 561 - 56
22chain 'A' and (resid 57 through 91 )57 - 9157 - 91
33chain 'A' and (resid 92 through 134 )92 - 13492 - 134
44chain 'A' and (resid 135 through 202 )135 - 202135 - 202
55chain 'A' and (resid 203 through 221 )203 - 221203 - 221
66chain 'A' and (resid 222 through 298 )222 - 298222 - 298

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