[English] 日本語
Yorodumi
- PDB-5wd8: Crystal structure of Legionella pneumophila effector lpg2328 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wd8
TitleCrystal structure of Legionella pneumophila effector lpg2328
ComponentsLem22
KeywordsPROTEIN BINDING / bacterial effector / Legionella / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.944 Å
AuthorsKozlov, G. / Wong, K. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proteins / Year: 2018
Title: Crystal structure of the Legionella effector Lem22.
Authors: Kozlov, G. / Wong, K. / Gehring, K.
History
DepositionJul 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: citation / entity / entity_name_com
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lem22
B: Lem22


Theoretical massNumber of molelcules
Total (without water)21,3412
Polymers21,3412
Non-polymers00
Water3,135174
1
A: Lem22


Theoretical massNumber of molelcules
Total (without water)10,6711
Polymers10,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lem22


Theoretical massNumber of molelcules
Total (without water)10,6711
Polymers10,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.044, 81.143, 45.684
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lem22 / lpg2328


Mass: 10670.622 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_2320 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G8UTY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.988 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.94→40.575 Å / Num. obs: 12194 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rsym value: 0.135 / Net I/σ(I): 19.9
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1083 / Rsym value: 0.506 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.944→40.572 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.04
RfactorNum. reflection% reflection
Rfree0.2699 588 4.82 %
Rwork0.2161 --
obs0.2186 12194 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.944→40.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 174 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011474
X-RAY DIFFRACTIONf_angle_d0.3341974
X-RAY DIFFRACTIONf_dihedral_angle_d6.107926
X-RAY DIFFRACTIONf_chiral_restr0.026226
X-RAY DIFFRACTIONf_plane_restr0.002250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9444-1.980.32821500.24342766X-RAY DIFFRACTION95
2.14-2.44970.28241650.2262895X-RAY DIFFRACTION100
2.4497-3.08620.28221340.23682950X-RAY DIFFRACTION100
3.0862-4.18760.24341390.19592995X-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)
10.31970.0599-0.07770.20110.20270.38570.0262-0.1015-0.051-0.01910.0266-0.12380.01970.193200.20670.0062-0.00420.1723-0.01840.1981-6.4065-1.3208-11.4545
20.0198-0.0860.01550.50140.03380.0866-0.34140.0581-0.2651-0.16160.04450.49820.24680.2694-0.00530.32170.07310.04350.35820.03170.2116-14.8493-3.83555.9286
30.5667-0.2143-0.02330.18330.21210.3759-0.12260.1876-0.09420.0924-0.25370.2660.065-0.3517-0.01040.18120.00030.00450.2295-0.00510.2223-14.9757-3.6784-17.1636
40.0191-0.05230.00910.15890.03290.14030.0847-0.153-0.2379-0.1396-0.03360.0940.2417-0.1524-0.0080.2343-0.008-0.02910.22280.01790.2052-4.8293-25.667-9.8704
50.111-0.0817-0.05910.07250.09360.1666-0.1452-0.1440.25380.0377-0.03820.10510.0292-0.2146-0.01440.22120.01060.01530.19360.00230.2595-2.583-17.6265-7.4826
60.525-0.1569-0.00730.2237-0.29070.4292-0.11280.0971-0.08420.0278-0.159-0.24840.05490.2453-0.0020.19480.0048-0.01310.2213-0.00630.22933.5486-19.2101-17.234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 96 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 63 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 97 )

+
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