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- PDB-7w3s: The complex structure of Larg1-ADPr from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 7w3s
TitleThe complex structure of Larg1-ADPr from Legionella pneumophila
ComponentsType IV secretion protein Dot
KeywordsHYDROLASE / Legionella pneumophila effector complex / ADPr
Function / homologyChem-AR6 / Type IV secretion protein Dot
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.324 Å
AuthorsOuyang, S. / Guan, H. / Li, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: mLife / Year: 2022
Title: Legionella pneumophila temporally regulates the activity of ADP/ATP translocases by reversible ADP-ribosylation.
Authors: Fu, J. / Li, P. / Guan, H. / Huang, D. / Song, L. / Ouyang, S. / Luo, Z.Q.
History
DepositionNov 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type IV secretion protein Dot
B: Type IV secretion protein Dot
C: Type IV secretion protein Dot
D: Type IV secretion protein Dot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,3878
Polymers188,1504
Non-polymers2,2374
Water12,701705
1
B: Type IV secretion protein Dot
C: Type IV secretion protein Dot
D: Type IV secretion protein Dot
hetero molecules

A: Type IV secretion protein Dot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,3878
Polymers188,1504
Non-polymers2,2374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area8560 Å2
ΔGint-45 kcal/mol
Surface area61290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.250, 92.812, 116.053
Angle α, β, γ (deg.)90.000, 105.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type IV secretion protein Dot


Mass: 47037.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_15620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F197
#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.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 289.15 K / Method: counter-diffusion
Details: 0.2M Lithium sulfate, 0.1M Tris, pH 7.5, 5% polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.32→53.42 Å / Num. obs: 94202 / % possible obs: 97.54 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 12.09
Reflection shellResolution: 2.324→2.407 Å / Num. unique obs: 9251 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
HKL-3000phasing
SHELXSphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.324→53.416 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 4600 4.89 %
Rwork0.186 89461 -
obs0.188 94061 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.79 Å2 / Biso mean: 42.2779 Å2 / Biso min: 18.52 Å2
Refinement stepCycle: final / Resolution: 2.324→53.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13334 0 0 705 14039
Biso mean---43.2 -
Num. residues----1652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813701
X-RAY DIFFRACTIONf_angle_d1.05418582
X-RAY DIFFRACTIONf_chiral_restr0.0582001
X-RAY DIFFRACTIONf_plane_restr0.0072375
X-RAY DIFFRACTIONf_dihedral_angle_d7.1288090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.324-2.35030.33181390.272286595
2.3503-2.3780.31811380.2682295796
2.378-2.4070.33341690.2529298199
2.407-2.43740.31651530.23463057100
2.4374-2.46950.281630.22693059100
2.4695-2.50330.31061470.21693038100
2.5033-2.53910.25351580.2113020100
2.5391-2.5770.27231510.21353085100
2.577-2.61730.24751420.21572990100
2.6173-2.66020.28431380.2229301097
2.6602-2.7060.23840.2209134845
2.706-2.75520.31221590.22193034100
2.7552-2.80820.25631690.21063062100
2.8082-2.86560.27391400.20253040100
2.8656-2.92790.24841660.20353037100
2.9279-2.9960.25521300.20293074100
2.996-3.07090.23921700.19773028100
3.0709-3.15390.26141520.20213044100
3.1539-3.24670.23371450.20073092100
3.2467-3.35150.23941600.19973020100
3.3515-3.47120.24731700.19153046100
3.4712-3.61020.2341760.18763053100
3.6102-3.77440.21071450.17033077100
3.7744-3.97340.18161330.15223083100
3.9734-4.22220.18521840.14553045100
4.2222-4.54810.17851480.14453075100
4.5481-5.00550.18961680.14423067100
5.0055-5.7290.19281810.16163074100
5.729-7.21520.19031470.19063122100
7.2152-53.40.20691750.1893297895

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