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- PDB-5m3e: Macrodomain of Thermus aquaticus DarG in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 5m3e
TitleMacrodomain of Thermus aquaticus DarG in complex with ADP-ribose
ComponentsAppr-1-p processing domain protein
KeywordsANTITOXIN / macrodomain / ADP-ribosylation / ADP-ribose / toxin-antitoxin
Function / homologyAppr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / ADENOSINE-5-DIPHOSPHORIBOSE / Appr-1-p processing domain protein
Function and homology information
Biological speciesThermus aquaticus Y51MC23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAriza, A.
CitationJournal: Mol. Cell / Year: 2016
Title: The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA.
Authors: Jankevicius, G. / Ariza, A. / Ahel, M. / Ahel, I.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Appr-1-p processing domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3793
Polymers18,7851
Non-polymers5952
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-21 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.410, 60.392, 76.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Appr-1-p processing domain protein


Mass: 18784.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: codon optimised gene / Source: (gene. exp.) Thermus aquaticus Y51MC23 (bacteria) / Gene: TaqDRAFT_4250 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta (DE3) / References: UniProt: B7A854
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium bromide and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→60.39 Å / Num. obs: 6306 / % possible obs: 98.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 25
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 7 / CC1/2: 0.992 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DX6

2dx6


Resolution: 2.5→47.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.395 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.62 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24375 313 5 %RANDOM
Rwork0.1946 ---
obs0.19695 5955 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.825 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å2-0 Å2-0 Å2
2---3.58 Å20 Å2
3---8.22 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 37 17 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191299
X-RAY DIFFRACTIONr_bond_other_d0.0020.021253
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9991769
X-RAY DIFFRACTIONr_angle_other_deg0.9932873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94322.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91715214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8911514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5123.598611
X-RAY DIFFRACTIONr_mcbond_other1.5093.594610
X-RAY DIFFRACTIONr_mcangle_it2.5785.385763
X-RAY DIFFRACTIONr_mcangle_other2.5775.39764
X-RAY DIFFRACTIONr_scbond_it1.5243.791688
X-RAY DIFFRACTIONr_scbond_other1.5233.792689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.635.6041005
X-RAY DIFFRACTIONr_long_range_B_refined4.70328.0311363
X-RAY DIFFRACTIONr_long_range_B_other4.70428.0261362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 22 -
Rwork0.188 360 -
obs--83.77 %
Refinement TLS params.Method: refined / Origin x: -10.435 Å / Origin y: -7.774 Å / Origin z: 13.137 Å
111213212223313233
T0.101 Å20.0024 Å20.0226 Å2-0.0227 Å20.0176 Å2--0.0841 Å2
L2.1977 °2-0.5975 °2-0.7115 °2-6.0956 °20.3883 °2--0.7636 °2
S0.1137 Å °0.0609 Å °-0.154 Å °-0.2823 Å °-0.027 Å °-0.4687 Å °-0.0948 Å °-0.1188 Å °-0.0867 Å °

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