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- PDB-8dmu: Crystal structure of macrodomain CG3568 from Drosophila melanogas... -

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Basic information

Entry
Database: PDB / ID: 8dmu
TitleCrystal structure of macrodomain CG3568 from Drosophila melanogaster in complex with ADP-ribose
ComponentsCG3568
KeywordsHYDROLASE / Macrodomain / ADP-ribose / Complex / Glycohydrolase
Function / homologyProtein of unknown function DUF4804 / ADP-ribosylhydrolase MavL-like / ADP-ribosylarginine hydrolase activity / Chem-AR6 / NICKEL (II) ION / AT21585p
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Nat Commun / Year: 2024
Title: Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain.
Authors: Zhang, Z. / Fu, J. / Rack, J.G.M. / Li, C. / Voorneveld, J. / Filippov, D.V. / Ahel, I. / Luo, Z.Q. / Das, C.
History
DepositionJul 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG3568
B: CG3568
C: CG3568
D: CG3568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,92026
Polymers220,3924
Non-polymers3,52822
Water25,4011410
1
A: CG3568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0758
Polymers55,0981
Non-polymers9777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CG3568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1119
Polymers55,0981
Non-polymers1,0138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CG3568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8494
Polymers55,0981
Non-polymers7513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CG3568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8855
Polymers55,0981
Non-polymers7874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.048, 129.805, 199.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CG3568 / AT21585p


Mass: 55098.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG3568, CG3568, Dmel_CG3568 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W4J9

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Non-polymers , 5 types, 1432 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.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1410 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.5, 1 M lithium sulfate, 0.01 M nickel (II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→92.25 Å / Num. obs: 182007 / % possible obs: 99.82 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.41
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 17977 / CC1/2: 0.744

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold AT21585p

Resolution: 2→92.25 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 8992 4.95 %
Rwork0.2317 172786 -
obs0.2338 181778 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.17 Å2 / Biso mean: 32.675 Å2 / Biso min: 15.64 Å2
Refinement stepCycle: final / Resolution: 2→92.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14848 0 202 1452 16502
Biso mean--34.11 37 -
Num. residues----1901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.36442860.327356535939100
2.02-2.050.34722670.305257736040100
2.05-2.070.35852880.295357015989100
2.07-2.10.31762960.284257196015100
2.1-2.130.31423270.267157196046100
2.13-2.150.31822740.261956945968100
2.15-2.190.32843070.268657386045100
2.19-2.220.32282810.266857466027100
2.22-2.250.30752640.260357335997100
2.25-2.290.31162880.25657216009100
2.29-2.330.28662800.254957296009100
2.33-2.370.3043000.252557406040100
2.37-2.420.32633000.249157196019100
2.42-2.470.30742820.246457546036100
2.47-2.520.27533020.253157556057100
2.52-2.580.30613160.255956735989100
2.58-2.640.28653100.259457656075100
2.64-2.710.2943150.245457016016100
2.71-2.790.28662910.2557666057100
2.79-2.880.2943130.243757946107100
2.88-2.990.29362920.247757366028100
2.99-3.110.28442970.247157596056100
3.11-3.250.31423380.238257646102100
3.25-3.420.28172990.21757656064100
3.42-3.630.24663090.203457996108100
3.63-3.910.22363320.19257616093100
3.91-4.310.2133110.184158356146100
4.31-4.930.20733230.180758366159100
4.93-6.210.23942970.214959246221100
6.21-92.250.27513070.23816014632198
Refinement TLS params.Method: refined / Origin x: 34.9876 Å / Origin y: 0.1021 Å / Origin z: 3.5652 Å
111213212223313233
T0.1723 Å20.0039 Å20.0021 Å2-0.1727 Å20.0081 Å2--0.2203 Å2
L0.2133 °2-0.1946 °2-0.0564 °2-0.2588 °20.087 °2--0.3046 °2
S-0.0913 Å °-0.0465 Å °-0.0077 Å °0.0815 Å °0.054 Å °-0.0072 Å °0.0366 Å °0.0245 Å °0.0381 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 601
2X-RAY DIFFRACTION1allB25 - 601
3X-RAY DIFFRACTION1allC24 - 601
4X-RAY DIFFRACTION1allD24 - 601
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allF1 - 10
7X-RAY DIFFRACTION1allG1 - 6
8X-RAY DIFFRACTION1allS1 - 1631

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