[English] 日本語
Yorodumi
- PDB-8dmr: Legionella macrodomain effector MavL R370A in complex with ADP-ribose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dmr
TitleLegionella macrodomain effector MavL R370A in complex with ADP-ribose
ComponentsMavL
KeywordsANTITOXIN / Complex / Macrodomain / Metaeffector
Function / homologyChem-AR6 / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsZhang, Z. / Das, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM126296 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI148103 United States
CitationJournal: To Be Published
Title: Structure of ADP-ribose-bound Legionella pneumophila macrodomain effector MavL R370A
Authors: Zhang, Z. / Das, C.
History
DepositionJul 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0037
Polymers44,0951
Non-polymers9096
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.557, 95.557, 54.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein MavL


Mass: 44094.547 Da / Num. of mol.: 1 / Mutation: R370A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSJ1

-
Non-polymers , 6 types, 304 molecules

#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.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.86→42.21 Å / Num. obs: 41115 / % possible obs: 99.65 % / Redundancy: 4.6 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.998 / Net I/σ(I): 23.61
Reflection shellResolution: 1.86→1.927 Å / Num. unique obs: 4087 / CC1/2: 0.781

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMI

6omi


Resolution: 1.86→42.21 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1798 2031 4.94 %
Rwork0.1506 39043 -
obs0.152 41074 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.04 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 57 298 3214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122995
X-RAY DIFFRACTIONf_angle_d1.21924075
X-RAY DIFFRACTIONf_chiral_restr0.0616444
X-RAY DIFFRACTIONf_plane_restr0.0089525
X-RAY DIFFRACTIONf_dihedral_angle_d15.1539434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.28041220.23922558X-RAY DIFFRACTION98.24
1.9-1.950.22011490.20712589X-RAY DIFFRACTION99.89
1.95-20.2371590.2122572X-RAY DIFFRACTION100
2-2.060.22511120.18582599X-RAY DIFFRACTION99.93
2.06-2.130.20071350.17462596X-RAY DIFFRACTION99.71
2.13-2.20.23641320.1722553X-RAY DIFFRACTION98.71
2.2-2.290.19881380.16512606X-RAY DIFFRACTION99.89
2.29-2.40.20941540.16122580X-RAY DIFFRACTION100
2.4-2.520.22131130.16492609X-RAY DIFFRACTION99.82
2.52-2.680.21291660.1642584X-RAY DIFFRACTION99.93
2.68-2.890.18521210.172646X-RAY DIFFRACTION99.86
2.89-3.180.20641260.16532604X-RAY DIFFRACTION99.42
3.18-3.640.18231170.14052645X-RAY DIFFRACTION99.78
3.64-4.580.13131550.11452617X-RAY DIFFRACTION99.6
4.58-42.210.14951320.13732685X-RAY DIFFRACTION98.91
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)
12.7600447953-1.31926844435-0.4787715411852.565056624920.4217699458222.994688494070.0742909187354-0.2619236341060.2679293932950.09531209456890.331217708543-0.6104574395440.211656770980.520270991427-0.3420711296010.2572486263150.0162169856311-0.04608181976330.280241397123-0.1307136726870.45702295843114.921649555933.2311807589-2.30790362744
23.09693463127-1.02777880141-0.06759504689842.96558283720.7043149141142.442060007430.06177134740810.138889929597-0.0471176367623-0.125517196470.075842958093-0.2842055920210.2997657196640.0827986416345-0.1458420688870.329078137306-0.00243526403579-0.00835102610730.211406028527-0.0306199884160.2364653115595.207813972526.4782436456-6.83253535546
32.521725609120.422424305138-0.2160101005562.268747711680.4543530791922.267836433190.142993684264-0.196429250984-0.3173371459650.715720194820.15844559076-0.2220284742241.056747533930.239753199482-0.2639241136780.6315579672010.0684308216821-0.1086548629340.2558466859130.003601256710370.3451662845563.1228401064920.451393472611.54762261
42.04840464958-0.7592093141780.1175968344614.8499874297-0.3325370507212.79461177065-0.00802659522266-0.0423701597880.06430071478510.08685023278240.0600767935562-0.1032494670910.0699501167545-0.192890394741-0.04073000392120.235304569914-0.005411827224460.001218628674910.243054124379-0.03003118114170.20582315829-3.3126912865935.90676212064.92041525788
52.710494740260.350738786688-0.03034661315315.29767495564-0.4790947719633.732325817230.0402198269684-0.1642806919660.06579433370340.2974782374610.0193526106339-0.0216139819678-0.0199778769019-0.228768280142-0.04939497954360.2596412491130.02461637633750.01480439906990.28380198795-0.02138977271070.253646847232-6.6174319465540.346101985510.152481171
61.43881351639-1.00088382014-0.5236895991393.326234417160.9586030035492.563623095030.07697856668510.1127180279830.01843975647810.0763984821214-0.1292362825740.4889556268550.0101588553188-0.637133358180.07201168998680.233667241763-0.02711001239530.0001777174435130.3499750677510.007124363396570.316816219953-13.119576901937.01328474862.17636869106
74.23804572535-0.320785614239-0.6521479182673.59506444273-0.3542672267013.556985482410.04163510190810.582743781904-0.185206201794-0.584972268689-0.1299902308760.3342081518130.234932915493-0.4503348220150.09826583470520.419349233547-0.0427138480849-0.08696925013540.400795659549-0.05341479647210.29626884723-10.065723866226.6761115395-16.2215622161
84.33177482532-1.27515498937-0.87086947053.241092955350.9139052865664.598594645030.1570714500910.3071345325710.0432114897773-0.4498871878190.334838082435-0.697404516510.02834264121340.380262810821-0.4486260651370.335428544090.04707020949630.07942316188190.1597844418420.08692443486350.2554925261766.5489876384832.4864925615-10.7939383732
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 64 )37 - 641 - 28
22chain 'A' and (resid 65 through 160 )65 - 16029 - 125
33chain 'A' and (resid 161 through 185 )161 - 185126 - 150
44chain 'A' and (resid 186 through 235 )186 - 235151 - 200
55chain 'A' and (resid 236 through 263 )236 - 263201 - 228
66chain 'A' and (resid 264 through 321 )264 - 321229 - 286
77chain 'A' and (resid 322 through 369 )322 - 369287 - 334
88chain 'A' and (resid 370 through 409 )370 - 409335 - 374

+
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