[English] 日本語
Yorodumi
- PDB-3tu3: 1.92 Angstrom resolution crystal structure of the full-length Spc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tu3
Title1.92 Angstrom resolution crystal structure of the full-length SpcU in complex with full-length ExoU from the type III secretion system of Pseudomonas aeruginosa
Components
  • ExoU
  • ExoU chaperone
KeywordsTOXIN/TOXIN CHAPERONE / type III secretion system / Pseudomonas aeruginosa / ExoU / SpcU / Infectious Diseases / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / SpcU- chaperone / ExoU - phospholipase A2 / TOXIN-TOXIN CHAPERONE complex
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
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.92 Å
AuthorsHalavaty, A.S. / Borek, D. / Otwinowski, Z. / Minasov, G. / Veesenmeyer, J.L. / Tyson, G. / Shuvalova, L. / Hauser, A.R. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos One / Year: 2012
Title: Structure of the Type III Secretion Effector Protein ExoU in Complex with Its Chaperone SpcU.
Authors: Halavaty, A.S. / Borek, D. / Tyson, G.H. / Veesenmeyer, J.L. / Shuvalova, L. / Minasov, G. / Otwinowski, Z. / Hauser, A.R. / Anderson, W.F.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ExoU chaperone
B: ExoU


Theoretical massNumber of molelcules
Total (without water)94,4392
Polymers94,4392
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-12 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.140, 52.583, 119.539
Angle α, β, γ (deg.)90.00, 126.59, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ExoU chaperone / SpcU


Mass: 17675.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: EXA77, EXC3, RS15, spcU / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: O66100
#2: Protein ExoU / PepA / Type III effector protein / Type three secretion effector protein


Mass: 76763.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: EXC2, exoU, pepA, RS14 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: O34208
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: The Classics H6 condition. ExoU - 87 uM; SpcU - 174 uM. , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D11.06899
SYNCHROTRONAPS 19-ID20.97721
SYNCHROTRONAPS 21-ID-F30.97872
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMar 31, 2011Mirror
ADSC QUANTUM 315r2CCDJul 11, 2011mirror
MARMOSAIC 225 mm CCD3CCDApr 14, 2011Be-Lenses/Diamond Laue Mono
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)ChannelSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
3Diamond[111]SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.068991
20.977211
30.978721
ReflectionResolution: 1.92→30 Å / Num. all: 59644 / Num. obs: 59644 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.87
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.65 / Num. unique all: 3000 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
SBC-Collectdata collection
SHELXDphasing
BUCCANEERmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.92→29.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.554 / SU ML: 0.088 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22459 2975 5 %RANDOM
Rwork0.19124 ---
obs0.19297 56018 99.8 %-
all-56018 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.06 Å2
2--0.25 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4937 0 0 490 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225276
X-RAY DIFFRACTIONr_bond_other_d0.0010.023602
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9787189
X-RAY DIFFRACTIONr_angle_other_deg0.85138810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.45692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.02924.174242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.315918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.811550
X-RAY DIFFRACTIONr_chiral_restr0.0890.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
X-RAY DIFFRACTIONr_mcbond_it0.8951.53377
X-RAY DIFFRACTIONr_mcbond_other0.2281.51351
X-RAY DIFFRACTIONr_mcangle_it1.62725448
X-RAY DIFFRACTIONr_scbond_it2.46731899
X-RAY DIFFRACTIONr_scangle_it4.0844.51741
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 212 -
Rwork0.225 4088 -
obs-4088 99.91 %
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)
10.8444-0.37770.33631.2492-1.41242.1778-0.03580.0384-0.1548-0.1232-0.0728-0.05230.26460.09450.10860.22790.01320.0730.1972-0.00630.151981.520234.431911.4118
21.8255-0.1561-0.05921.52470.03570.88670.04540.1883-0.0346-0.0795-0.04530.15530.0557-0.0976-0.00010.11150.0076-0.00560.03350.01320.10270.809129.631738.1634
31.5894-0.43070.09190.7585-0.17360.85010.14890.3468-0.1554-0.1081-0.09670.0940.0049-0.0624-0.05230.11840.0229-0.00860.1616-0.02930.161540.205146.771326.3006
40.8897-0.053-0.27922.78590.2660.8189-0.002-0.02150.01550.1085-0.00660.143-0.0317-0.03760.00870.07470.00310.01020.003-0.00430.064670.127355.297348.5154
50.56660.13631.03320.31840.23456.2508-0.03510.24530.014-0.0506-0.008-0.0107-0.1349-0.22860.04320.17470.0249-0.00110.2482-0.00340.11164.777856.84916.9281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B55 - 101
3X-RAY DIFFRACTION2B472 - 502
4X-RAY DIFFRACTION3B102 - 471
5X-RAY DIFFRACTION4B503 - 588
6X-RAY DIFFRACTION5B589 - 683

+
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