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- PDB-8dmt: Crystal structure of macrodomain CG2909 from Drosophila melanogas... -

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Basic information

Entry
Database: PDB / ID: 8dmt
TitleCrystal structure of macrodomain CG2909 from Drosophila melanogaster in complex with ADP-ribose
ComponentsRE54994p
KeywordsHYDROLASE / Macrodomain / ADP-ribose / Complex / Glycohydrolase
Function / homologyProtein of unknown function DUF4804 / ADP-ribosylhydrolase MavL-like / ADP-ribosylarginine hydrolase activity / Chem-AR6 / RE54994p
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RE54994p
B: RE54994p
C: RE54994p
D: RE54994p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,1478
Polymers221,9104
Non-polymers2,2374
Water8,251458
1
A: RE54994p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0372
Polymers55,4771
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RE54994p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0372
Polymers55,4771
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RE54994p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0372
Polymers55,4771
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RE54994p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0372
Polymers55,4771
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.949, 90.006, 212.267
Angle α, β, γ (deg.)90.000, 95.890, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
RE54994p


Mass: 55477.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG2909, CG2909, Dmel_CG2909 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W2W5
#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.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ammonium citrate, 12% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→38.49 Å / Num. obs: 77326 / % possible obs: 92.21 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.77 Å2 / CC1/2: 0.984 / Net I/σ(I): 8.9
Reflection shellResolution: 2.28→2.362 Å / Num. unique obs: 5609 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold RE54994p

Resolution: 2.28→38.49 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 3115 2.64 %
Rwork0.1957 115101 -
obs0.1967 77255 71.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.54 Å2 / Biso mean: 33.9878 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: final / Resolution: 2.28→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15227 0 144 459 15830
Biso mean--28.31 32.44 -
Num. residues----1950
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.310.3853460.3391182925
2.31-2.350.3526780.3013277138
2.35-2.390.3842890.2979305142
2.39-2.430.3898890.2786328344
2.43-2.480.3083810.2635314844
2.48-2.530.3206980.2569372751
2.53-2.590.34771150.2539408756
2.59-2.650.25991170.2519421358
2.65-2.710.25441280.2352473464
2.71-2.790.29821300.2304486068
2.79-2.870.26351490.2223543773
2.87-2.960.27621560.2191574379
2.96-3.070.24361670.2246622085
3.07-3.190.28891680.2159618785
3.19-3.330.2471810.2061645288
3.33-3.510.24132020.1955712497
3.51-3.730.27581800.2121683394
3.73-4.020.25911820.1738700296
4.02-4.420.15561930.1443730899
4.42-5.060.16571800.1505685294
5.06-6.370.20891980.177726699
6.37-38.490.17591880.1646697496
Refinement TLS params.Method: refined / Origin x: -17.1861 Å / Origin y: 26.1761 Å / Origin z: 52.6157 Å
111213212223313233
T0.18 Å2-0.0093 Å2-0.009 Å2-0.1742 Å2-0.008 Å2--0.1777 Å2
L0.0331 °2-0.0011 °20.014 °2-0.0053 °2-0.039 °2--0.2297 °2
S0.0148 Å °0.0131 Å °0.0009 Å °0.014 Å °-0.0167 Å °0.0047 Å °-0.0087 Å °0.0097 Å °0.0033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 501
2X-RAY DIFFRACTION1allB11 - 501
3X-RAY DIFFRACTION1allC11 - 501
4X-RAY DIFFRACTION1allD11 - 501
5X-RAY DIFFRACTION1allS1 - 472

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