[English] 日本語
Yorodumi
- PDB-6omi: Crystal structure of the Legionella effector protein MavL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6omi
TitleCrystal structure of the Legionella effector protein MavL
ComponentsMavL
KeywordsHYDROLASE / ADP-ribosyltransferase (ART) / macrodomain / Secreted bacterial effector protein
Function / homologyMacrodomain effector MavL / ADP-D-ribose binding / host cell cytoplasm / extracellular region / BROMIDE ION / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.643 Å
AuthorsCygler, M. / Voth, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)412613 Canada
CitationJournal: To Be Published
Title: Crystal Structure of the Legionella Effector protein MavL
Authors: Cygler, M. / Voth, K.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MavL
B: MavL
C: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4305
Polymers133,2703
Non-polymers1602
Water25214
1
A: MavL
B: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9273
Polymers88,8472
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-20 kcal/mol
Surface area27770 Å2
MethodPISA
2
C: MavL
hetero molecules

C: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0064
Polymers88,8472
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area2330 Å2
ΔGint-21 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.619, 138.009, 108.523
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-501-

BR

21C-605-

HOH

-
Components

#1: Protein MavL


Mass: 44423.336 Da / Num. of mol.: 3 / Fragment: residues 42-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2526 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZSJ1
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.5

-
Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.993054 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993054 Å / Relative weight: 1
ReflectionResolution: 2.643→48.77 Å / Num. obs: 41740 / % possible obs: 99.26 % / Redundancy: 1.998 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.53
Reflection shellResolution: 2.643→2.738 Å / Rmerge(I) obs: 1.387 / Num. unique obs: 4058

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.643→45.14 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1249 2.99 %
Rwork0.2114 --
obs0.2126 41718 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.643→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 2 14 8108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028296
X-RAY DIFFRACTIONf_angle_d0.56411319
X-RAY DIFFRACTIONf_dihedral_angle_d14.3534841
X-RAY DIFFRACTIONf_chiral_restr0.0431240
X-RAY DIFFRACTIONf_plane_restr0.0041489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.643-2.74860.37611380.33414359X-RAY DIFFRACTION97
2.7486-2.87370.37231280.31294482X-RAY DIFFRACTION99
2.8737-3.02520.38071500.28764509X-RAY DIFFRACTION99
3.0252-3.21470.30781410.27924449X-RAY DIFFRACTION99
3.2147-3.46280.30751330.25154481X-RAY DIFFRACTION99
3.4628-3.81120.25061410.22094517X-RAY DIFFRACTION100
3.8112-4.36240.2571410.18134537X-RAY DIFFRACTION100
4.3624-5.49490.19271360.17734540X-RAY DIFFRACTION100
5.4949-48.770.2291410.19674595X-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)
14.1686-0.63350.73893.1318-0.12463.98530.2808-0.0151-0.53670.06040.0169-0.28130.6960.4112-0.22110.91540.4024-0.18110.6239-0.15530.863566.173842.81718.6459
23.21860.02990.92192.2782-0.22393.0124-0.0906-0.23380.246-0.2383-0.23580.2112-0.5479-0.74890.28210.73370.4361-0.02190.8609-0.13320.610851.69573.585226.6803
33.1610.30490.06572.7249-0.50793.04120.5005-1.63050.01770.3946-0.3461-0.23660.0977-0.1324-0.14920.5643-0.17350.01341.4148-0.00350.733682.805172.077166.3126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 41 through 404)
2X-RAY DIFFRACTION2(chain 'B' and resid 40 through 404)
3X-RAY DIFFRACTION3(chain 'C' and resid 40 through 403)

+
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