[English] 日本語
Yorodumi
- PDB-4akx: Structure of the heterodimeric complex ExoU-SpcU from the type II... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4akx
TitleStructure of the heterodimeric complex ExoU-SpcU from the type III secretion system (T3SS) of Pseudomonas aeruginosa
Components
  • EXOU
  • SPCU
KeywordsTRANSPORT PROTEIN / PHOSPHOLIPASE / CHAPERONE / TOXIN
Function / homology
Function and homology information


lipid catabolic process / hydrolase activity
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #80 / : / : / ExoU toxin, middle helical domain / ExoU toxin, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #100 / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Patatin-like phospholipase domain / Patatin-like phospholipase ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #80 / : / : / ExoU toxin, middle helical domain / ExoU toxin, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #100 / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Signal recognition particle alu RNA binding heterodimer, srp9/1 / Acyl transferase/acyl hydrolase/lysophospholipase / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Up-down Bundle / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ExoU / ExoU chaperone / ExoU / SpcU
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å
AuthorsGendrin, C. / Contreras-Martel, C. / Bouillot, S. / Elsen, S. / Lemaire, D. / Skoufias, D.A. / Huber, P. / Attree, I. / Dessen, A.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Basis of Cytotoxicity Mediated by the Type III Secretion Toxin Exou from Pseudomonas Aeruginosa
Authors: Gendrin, C. / Contreras-Martel, C. / Bouillot, S. / Elsen, S. / Lemaire, D. / Skoufias, D.A. / Huber, P. / Attree, I. / Dessen, A.
History
DepositionFeb 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SPCU
B: EXOU


Theoretical massNumber of molelcules
Total (without water)85,8292
Polymers85,8292
Non-polymers00
Water68538
1
A: SPCU
B: EXOU

A: SPCU
B: EXOU


Theoretical massNumber of molelcules
Total (without water)171,6574
Polymers171,6574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8940 Å2
ΔGint-39.2 kcal/mol
Surface area64550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.887, 52.799, 121.811
Angle α, β, γ (deg.)90.00, 127.18, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein SPCU


Mass: 13937.651 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: CLINICAL ISOLATE (GESPA 1999 COLLECTION) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02IF2, UniProt: O66100*PLUS
#2: Protein EXOU


Mass: 71890.961 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-687
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: CLINICAL ISOLATE (GESPA 1999 COLLECTION) / Description: GESPA 1999 COLLECTION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02IF1, UniProt: O34208*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHROMBIN SITE WAS INTRODUCED BETWEEN RESIDUES 29 AND 30 OF EXOU. THE DIGESTED PROTEIN WAS ...THROMBIN SITE WAS INTRODUCED BETWEEN RESIDUES 29 AND 30 OF EXOU. THE DIGESTED PROTEIN WAS CRYSTALLIZED IN COMPLEX WITH SPCU

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 9 / Details: 50 MM BICINE PH 9.0, 10% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.94→97.05 Å / Num. obs: 17008 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 82.666 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.94→97.05 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 42.898 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.26437 840 5 %RANDOM
Rwork0.20801 ---
obs0.21102 15943 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.814 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å2-0.51 Å2
2--0.73 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.94→97.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 0 38 5043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9956898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7535649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60624.123228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6115842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5921548
X-RAY DIFFRACTIONr_chiral_restr0.0870.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.941→3.018 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 40 -
Rwork0.315 930 -
obs--83.05 %
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)
12.7742.0978-0.15254.93753.25629.7772-0.30040.3906-0.4148-0.3413-0.0355-0.10360.4221-0.41040.33590.16640.01670.0460.28060.04780.179836.333537.619936.1173
21.9661.1056-0.02355.278-0.17172.8559-0.05630.1992-0.0251-0.0709-0.0352-0.453-0.01830.33020.09150.10870.00280.05650.152-0.01340.086149.929647.44883.5537
32.2430.5467-0.75461.4975-0.40022.72640.2316-0.5856-0.10670.3829-0.1955-0.4320.17360.4054-0.03620.5624-0.0117-0.05440.77020.02630.846279.048249.986622.4513
44.5393-1.27240.32575.222-3.548523.0410.0775-0.43970.62790.4107-0.4371-0.3888-0.69680.80510.35970.2026-0.1615-0.05430.289-0.0730.150954.468561.039235.5304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 121
2X-RAY DIFFRACTION1B28 - 33
3X-RAY DIFFRACTION1B50 - 66
4X-RAY DIFFRACTION2B67 - 102
5X-RAY DIFFRACTION2B473 - 601
6X-RAY DIFFRACTION3B103 - 472
7X-RAY DIFFRACTION4B602 - 685

+
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://pdbjlvh1.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