[English] 日本語
Yorodumi
- PDB-8ipw: The sturecture of Legionella effector protein MavL with ADPR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ipw
TitleThe sturecture of Legionella effector protein MavL with ADPR
ComponentsMavL
KeywordsPROTEIN BINDING / MavL / ADPR
Function / homologyChem-AR6 / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOuyang, S. / Guan, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172287 China
CitationJournal: Nat Commun / Year: 2024
Title: Legionella maintains host cell ubiquitin homeostasis by effectors with unique catalytic mechanisms.
Authors: Fu, J. / Li, S. / Guan, H. / Li, C. / Zhao, Y.B. / Chen, T.T. / Xian, W. / Zhang, Z. / Liu, Y. / Guan, Q. / Wang, J. / Lu, Q. / Kang, L. / Zheng, S.R. / Li, J. / Cao, S. / Das, C. / Liu, X. ...Authors: Fu, J. / Li, S. / Guan, H. / Li, C. / Zhao, Y.B. / Chen, T.T. / Xian, W. / Zhang, Z. / Liu, Y. / Guan, Q. / Wang, J. / Lu, Q. / Kang, L. / Zheng, S.R. / Li, J. / Cao, S. / Das, C. / Liu, X. / Song, L. / Ouyang, S. / Luo, Z.Q.
History
DepositionMar 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _audit_author.name / _chem_comp.name ..._audit_author.name / _chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MavL
B: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9074
Polymers80,7892
Non-polymers1,1192
Water27015
1
A: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9542
Polymers40,3941
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9542
Polymers40,3941
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.790, 108.320, 129.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MavL


Mass: 40394.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12725 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2R2
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 289.15 K / Method: counter-diffusion
Details: 0.25 M potassium citrate tribasic monohydrate,18%PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→29.11 Å / Num. obs: 30117 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 1970 / CC1/2: 0.609

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMI

6omi


Resolution: 2.35→25.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.432 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.419 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1998 6.63 %RANDOM
Rwork0.2095 ---
obs0.2126 30117 98.4 %-
Displacement parametersBiso mean: 74.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.9453 Å20 Å20 Å2
2--18.0131 Å20 Å2
3----16.0679 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.35→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5588 0 72 16 5676
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1945SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes972HARMONIC5
X-RAY DIFFRACTIONt_it5802HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion20.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4338SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.37 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3033 -6.63 %
Rwork0.3172 563 -
all0.3162 603 -
obs--99.01 %
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)
13.5054-1.2747-0.18322.20060.45030.510.07590.25560.3263-0.0833-0.0621-0.3829-0.07370.1047-0.0138-0.093-0.03420.1058-0.10070.06110.1553-19.2433-0.3188-6.796
22.155-0.89930.19382.52480.3641.1777-0.1163-0.34230.41650.3748-0.0143-0.38730.01630.16830.1306-0.0522-0.0506-0.0074-0.1147-0.09290.2104-22.54167.684510.9255
31.4198-0.0849-0.60421.12031.37261.76230.0520.12560.374-0.0137-0.1417-0.0345-0.078-0.04180.08970.0063-0.01080.0733-0.15570.02530.2975-33.72378.73920.0874
41.6682-0.4802-0.10512.04520.92351.46590.00270.63690.3486-0.3153-0.13350.0082-0.1415-0.03010.1309-0.0457-0.00510.0853-0.13820.16070.1383-30.57015.1773-12.8835
52.062.3537-0.4017.7532-0.52680.27720.1262-0.1983-0.0734-0.0966-0.0395-0.08560.1429-0.0402-0.08670.0931-0.018-0.04720.00130.0418-0.2065-27.738814.7217-42.9833
61.79650.4596-0.30933.0359-0.93881.09560.3593-0.4330.22150.4304-0.2639-0.1391-0.1517-0.0915-0.09530.0609-0.1488-0.00640.0812-0.1123-0.2003-26.510628.4393-31.8687
72.39721.30750.38124.0704-0.71452.07740.15290.16690.0458-0.874-0.4096-0.78330.48150.40230.25670.09210.13610.149-0.07370.0069-0.1184-18.516223.958-52.0937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|42 - A|161 }
2X-RAY DIFFRACTION2{ A|162 - A|282 }
3X-RAY DIFFRACTION3{ A|283 - A|347 }
4X-RAY DIFFRACTION4{ A|348 - A|404 }
5X-RAY DIFFRACTION5{ B|42 - B|161 }
6X-RAY DIFFRACTION6{ B|162 - B|347 }
7X-RAY DIFFRACTION7{ B|348 - B|402 }

+
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