[English] 日本語
Yorodumi
- PDB-6fzx: LasB, hydroxymate Inhibitor Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fzx
TitleLasB, hydroxymate Inhibitor Complex
ComponentsKeratinase KP2
KeywordsHYDROLASE / LasB / hydroxymate 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 / 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
Chem-EEK / Neutral metalloproteinase / Elastase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKO4116_3_1 Germany
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Tackling Pseudomonas aeruginosa Virulence by a Hydroxamic Acid-Based LasB Inhibitor.
Authors: Kany, A.M. / Sikandar, A. / Yahiaoui, S. / Haupenthal, J. / Walter, I. / Empting, M. / Kohnke, J. / Hartmann, R.W.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7326
Polymers33,1761
Non-polymers5575
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-24 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.727, 52.982, 122.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Keratinase KP2


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: E3ULB4, UniProt: P14756*PLUS

-
Non-polymers , 6 types, 301 molecules

#2: Chemical ChemComp-EEK / ~{N}-(3,4-dichlorophenyl)-~{N}'-oxidanyl-propanediamide


Mass: 263.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8Cl2N2O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 1.8 M AMSO4 and 0.1 M Tris-Cl, pH 8.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.738 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.738 Å / Relative weight: 1
ReflectionResolution: 2.1→61.26 Å / Num. obs: 16581 / % possible obs: 95.88 % / Redundancy: 2 % / Rmerge(I) obs: 0.1112 / Net I/σ(I): 4.46
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.3073

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZM

1ezm


Resolution: 2.1→61.26 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 820 4.95 %
Rwork0.179 --
obs0.1808 16573 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→61.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 29 296 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032406
X-RAY DIFFRACTIONf_angle_d0.5253260
X-RAY DIFFRACTIONf_dihedral_angle_d18.9841374
X-RAY DIFFRACTIONf_chiral_restr0.038324
X-RAY DIFFRACTIONf_plane_restr0.003432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23160.30771380.2162491X-RAY DIFFRACTION93
2.2316-2.40390.24881230.19212546X-RAY DIFFRACTION94
2.4039-2.64590.23061270.19182601X-RAY DIFFRACTION96
2.6459-3.02870.20471330.17762586X-RAY DIFFRACTION96
3.0287-3.81580.18861480.15892689X-RAY DIFFRACTION97
3.8158-61.28550.19071510.17292840X-RAY DIFFRACTION99
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)
10.13370.0469-0.09280.0271-0.0620.16420.00240.06770.01830.01520.0226-0.01540.02820.00870.00140.09830.0108-0.0060.10930.00350.100126.432259.77911.0277
20.08430.0205-0.10290.1137-0.06690.1119-0.01130.03060.00850.00460.0110.01440.00250.0120.00050.09470.00410.00080.1160.00130.094721.403159.779713.062
30.01020.02120.00630.0391-0.00630.05330.03050.00610.00970.06880.0715-0.05640.1369-0.11020.02090.10220.0062-0.00190.058-0.00090.09716.561851.614920.9688
40.13170.131-0.02950.3333-0.23810.19230.02970.0057-0.05930.0603-0.0296-0.0062-0.0110.03210.00850.06810.009-0.0030.06630.00610.075518.852649.593627.6123
50.0660.119-0.00380.2818-0.05070.05030.0441-0.05450.04120.21970.04540.3118-0.0205-0.13130.02430.1060.0220.03460.11280.05570.14952.709851.988929.2679
60.0246-0.00850.0090.05620.02890.02040.0782-0.0856-0.13810.08430.04260.09030.1123-0.10960.00730.139-0.0003-0.00820.12360.03390.14296.04943.072331.7721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 179 )
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 257 )
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 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