[English] 日本語
Yorodumi
- PDB-5ms7: Crystal structure of the legionella pneumophila effector protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ms7
TitleCrystal structure of the legionella pneumophila effector protein RavZ_20-502
ComponentsLegionella pneumophila effector protein RavZ
KeywordsHYDROLASE / Hydrolase / Autophagy / Legionella pneumophila effector protein / ATG8 deconjugating enzyme
Function / homology
Function and homology information


host intracellular membrane-bounded organelle / protein delipidation / symbiont-mediated suppression of host autophagy / phosphatidylinositol-3-phosphate binding / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane
Similarity search - Function
: / RavZ C-terminal PI3P-binding domain / RavZ catalytic domain
Similarity search - Domain/homology
: / Cysteine protease RavZ
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 33215 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPantoom, S. / Vetter, I.R. / Wu, Y.W.
CitationJournal: Elife / Year: 2017
Title: Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins.
Authors: Yang, A. / Pantoom, S. / Wu, Y.W.
History
DepositionDec 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
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: Legionella pneumophila effector protein RavZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8376
Polymers54,2861
Non-polymers5515
Water25214
1
A: Legionella pneumophila effector protein RavZ
hetero molecules

A: Legionella pneumophila effector protein RavZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,67412
Polymers108,5722
Non-polymers1,10210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
Buried area4290 Å2
ΔGint-29 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.770, 222.770, 72.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

-
Components

#1: Protein Legionella pneumophila effector protein RavZ


Mass: 54285.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 33215 (bacteria)
Gene: lpg1683 / Plasmid: pOPIN / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5ZUV9
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 16% PEG3350, 0.2 M BaCl2 and 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97862 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.8→47.15 Å / Num. obs: 22921 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 86.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1938 / Net I/σ(I): 15.14
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 26.3 % / Rmerge(I) obs: 1.951 / Mean I/σ(I) obs: 1.94 / CC1/2: 0.165 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQC

5cqc


Resolution: 2.8→47.145 Å / SU ML: 0.48 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 30.74
RfactorNum. reflection% reflection
Rfree0.2535 1146 5 %
Rwork0.2068 --
obs0.2091 22914 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 20 14 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092976
X-RAY DIFFRACTIONf_angle_d1.3794014
X-RAY DIFFRACTIONf_dihedral_angle_d17.0371103
X-RAY DIFFRACTIONf_chiral_restr0.052456
X-RAY DIFFRACTIONf_plane_restr0.006506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.92740.38621400.37092675X-RAY DIFFRACTION100
2.9274-3.08180.39651400.34042657X-RAY DIFFRACTION100
3.0818-3.27480.33991420.28222694X-RAY DIFFRACTION100
3.2748-3.52760.29051410.24012684X-RAY DIFFRACTION100
3.5276-3.88240.22461430.17482707X-RAY DIFFRACTION100
3.8824-4.44380.17871430.15712723X-RAY DIFFRACTION100
4.4438-5.59730.19891450.17662758X-RAY DIFFRACTION100
5.5973-47.15140.281520.20652870X-RAY DIFFRACTION100
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)
14.4951-1.65251.14098.50240.23869.0015-0.3255-0.26340.9135-0.19840.36380.2446-1.0762-0.3727-0.00110.86140.02590.03410.4250.01461.1955277.6274195.69989.3878
26.434-1.1194-1.01586.0979-0.26655.9837-0.23780.36620.0495-0.45430.1098-0.3098-0.50890.29130.08770.702-0.1349-0.04140.42920.02150.6217284.8119182.6046-4.5083
31.212-0.4078-0.45273.95693.79777.58730.15950.00570.5258-0.28250.0790.1049-1.86030.3571-0.32171.2527-0.1938-0.03030.4931-0.06641.2665281.489204.912222.1834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 432 )

+
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