[English] 日本語
Yorodumi
- PDB-9fs0: Pseudomonas aeruginosa Elastase in complex with a phosphonate bas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fs0
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: 1.3 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 phosphonate based inhibitor
Authors: Klein, A. / Hirsch, A.
History
DepositionJun 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6884
Polymers33,1761
Non-polymers5133
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area11690 Å2
Unit cell
Length a, b, c (Å)43.784, 50.044, 125.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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-A1IFY / [(2~{R})-4-methyl-1-oxidanylidene-1-[[2-(4-propan-2-yloxyphenyl)pyrimidin-5-yl]amino]pentan-2-yl]phosphonic acid


Mass: 407.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N3O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 6.5, 2.4 M Ammonium sulfate, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.89 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.3→32.95 Å / Num. obs: 68882 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 10.61 Å2 / CC1/2: 1 / Net I/σ(I): 25.77
Reflection shellResolution: 1.3→1.346 Å / Num. unique obs: 3368 / CC1/2: 0.973

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot1.19.2_4158model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→32.95 Å / SU ML: 0.1028 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1884 3399 4.93 %
Rwork0.172 65483 -
obs0.1728 68882 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.92 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 30 446 2793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992408
X-RAY DIFFRACTIONf_angle_d1.28863265
X-RAY DIFFRACTIONf_chiral_restr0.0918325
X-RAY DIFFRACTIONf_plane_restr0.0102432
X-RAY DIFFRACTIONf_dihedral_angle_d8.33338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.21021370.20172689X-RAY DIFFRACTION100
1.32-1.340.20821420.19552667X-RAY DIFFRACTION100
1.34-1.360.22231520.19242700X-RAY DIFFRACTION100
1.36-1.380.21541370.19522703X-RAY DIFFRACTION100
1.38-1.410.23451230.18932688X-RAY DIFFRACTION100
1.41-1.430.23321560.1942671X-RAY DIFFRACTION100
1.43-1.460.22371410.1942713X-RAY DIFFRACTION100
1.46-1.490.24541290.18932703X-RAY DIFFRACTION100
1.49-1.520.20771400.18592710X-RAY DIFFRACTION100
1.52-1.560.21721400.18532706X-RAY DIFFRACTION100
1.56-1.590.20381360.19232686X-RAY DIFFRACTION99.96
1.59-1.640.22221360.19032717X-RAY DIFFRACTION100
1.64-1.690.2491480.18462718X-RAY DIFFRACTION100
1.69-1.740.18981500.18442695X-RAY DIFFRACTION100
1.74-1.80.2171610.17852714X-RAY DIFFRACTION100
1.8-1.870.20421370.17792710X-RAY DIFFRACTION99.96
1.87-1.960.16431550.1672722X-RAY DIFFRACTION100
1.96-2.060.19391230.16072745X-RAY DIFFRACTION100
2.06-2.190.16781280.15372769X-RAY DIFFRACTION99.97
2.19-2.360.18841400.15032735X-RAY DIFFRACTION100
2.36-2.60.17441330.15912785X-RAY DIFFRACTION100
2.6-2.980.16521530.16662763X-RAY DIFFRACTION100
2.98-3.750.16281550.15672809X-RAY DIFFRACTION99.97
3.75-32.950.17581470.17872965X-RAY DIFFRACTION99.94
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)
14.36661977493-2.10236866876-4.061423774293.642666500453.069317327148.38586087755-0.03058260310220.06918106271690.01923222736630.0184262719015-0.1180131107320.26842641741-0.184797663985-0.241319735930.0812979312630.08758957019560.00359352072777-0.01776230063550.0415778200089-0.004630484623470.0980452844776-13.71712174672.445379652982.6726247408
21.199029118580.4189664321870.2381432455890.8056141011850.4039035213590.755142088810.005130181971340.0337983369488-0.00636153845135-0.0542183475134-0.004471106680220.0140629373737-0.02112665286490.0258896642210.0001257114881620.08134418928550.00882177660533-0.0008376890425780.067150580048-0.001495739645460.0682103166994-5.14886916528-5.485557160321.92201011743
32.970568061440.3040732192-1.377320971440.70585260250.376811781672.24815754525-0.06864004637560.122674652689-0.118907821683-0.02106265109530.034980733869-0.01051088296220.131779754404-0.05782297353840.0341385466520.07299169342410.0138862614121-0.01042645093020.03299317559410.01039263721960.0610373974164-1.3070588068-8.8028762755110.855102066
40.6262199352530.1695705329770.08558211962790.8475927380850.3671716883270.5279102222280.0184246235610.004699611040220.03350060377130.0036137976407-0.02107579720380.0169772645191-0.00380041102596-0.02779949814010.001415233963840.0891282457294-0.001925182947560.007444294741620.0810745142527-0.001348236520230.0806404638854-1.984167088731.1834169862318.3153748163
50.6022916677120.117634349528-0.2400397984651.2558123665-0.1560577068351.367644417750.00955915927139-0.000551721375720.009199746183720.03260510900190.0132260013049-0.0681735881343-0.008060985378240.0341292356646-0.02361415055110.0651822620428-0.00729429277165-0.006358041661230.0540771392663-0.01763718171660.07814015682957.532696815948.7796155428725.3954843034
61.213759478231.36504964101-0.8602285380512.62015680427-2.276329821045.280429161280.0481627120837-0.04845741758690.09388080703970.0484324476703-0.0435983092377-0.108492321187-0.1468234975680.173518015196-0.01430235705820.0765573748384-0.0002713848048970.004020138240860.0762279909924-0.02876213533930.11995952925112.704280316717.028529389827.0897561248
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 17 )1 - 171 - 17
22chain 'A' and (resid 18 through 91 )18 - 9118 - 91
33chain 'A' and (resid 92 through 112 )92 - 11292 - 112
44chain 'A' and (resid 113 through 202 )113 - 202113 - 202
55chain 'A' and (resid 203 through 279 )203 - 279203 - 279
66chain 'A' and (resid 280 through 298 )280 - 298280 - 298

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more