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- PDB-5m3i: Macrodomain of Mycobacterium tuberculosis DarG -

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Basic information

Entry
Database: PDB / ID: 5m3i
TitleMacrodomain of Mycobacterium tuberculosis DarG
ComponentsRNase III inhibitor
KeywordsANTITOXIN / macrodomain / ADP-ribosylation / ADP-ribose / toxin-antitoxin
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase activity / purine nucleoside metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA damage response / cytosol
Similarity search - Function
: / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
RNase III inhibitor / DNA ADP-ribosyl glycohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNase III inhibitor
B: RNase III inhibitor
C: RNase III inhibitor
D: RNase III inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3787
Polymers72,2714
Non-polymers1063
Water1,33374
1
A: RNase III inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1032
Polymers18,0681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNase III inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1032
Polymers18,0681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNase III inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1032
Polymers18,0681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNase III inhibitor


Theoretical massNumber of molelcules
Total (without water)18,0681
Polymers18,0681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.840, 75.450, 116.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: -1 - 150 / Label seq-ID: 9 - 160

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
RNase III inhibitor / Appr-1-p processing domain protein


Mass: 18067.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: bacmid / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A045JW26, UniProt: O53605*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 200 mM ammonium chloride 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: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.17→59.22 Å / Num. obs: 32503 / % possible obs: 99.2 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.2
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 13.2 % / Rmerge(I) obs: 2.302 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.658 / % possible all: 98.4

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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: 2.17→59.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 21.045 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25135 1564 4.8 %RANDOM
Rwork0.21183 ---
obs0.21375 30882 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.173 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å2-0 Å2-0 Å2
2---4.59 Å20 Å2
3---2.94 Å2
Refinement stepCycle: 1 / Resolution: 2.17→59.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 3 74 4745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194817
X-RAY DIFFRACTIONr_bond_other_d0.0070.024747
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9726541
X-RAY DIFFRACTIONr_angle_other_deg1.336310925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48423.93201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9115824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8431532
X-RAY DIFFRACTIONr_chiral_restr0.0840.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215443
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021057
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_it2.6244.4952442
X-RAY DIFFRACTIONr_mcbond_other2.6244.4942441
X-RAY DIFFRACTIONr_mcangle_it4.0356.7343049
X-RAY DIFFRACTIONr_mcangle_other4.0356.7353050
X-RAY DIFFRACTIONr_scbond_it3.0214.8662375
X-RAY DIFFRACTIONr_scbond_other3.0214.8662375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9297.1213486
X-RAY DIFFRACTIONr_long_range_B_refined6.9935.2925104
X-RAY DIFFRACTIONr_long_range_B_other6.9935.265098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A186680.05
12B186680.05
21A185940.06
22C185940.06
31A186880.05
32D186880.05
41B185780.06
42C185780.06
51B186200.06
52D186200.06
61C186640.05
62D186640.05
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 117 -
Rwork0.399 2223 -
obs--98.44 %
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)
12.77291.3497-2.04983.904-1.28892.934-0.0006-0.07060.1369-0.1104-0.107-0.22710.09080.02820.10760.1478-0.0159-0.11040.1437-0.0170.1871-24.454-0.9614.816
22.13310.2812-1.90964.6834-2.67545.02220.08650.0646-0.1136-0.1378-0.5753-0.5793-0.0331-0.04210.48880.1277-0.0068-0.08090.17520.03070.2-57.33516.01414.976
31.5217-0.5806-1.59572.97932.14523.2368-0.07650.2548-0.19410.4039-0.09290.0922-0.1087-0.13940.16940.351-0.03410.00230.0933-0.0380.1366-42.333-1.51143.865
42.05091.2299-2.78823.3349-2.48514.7929-0.2517-0.166-0.2377-0.2639-0.1301-0.1415-0.099-0.01990.38180.35650.1448-0.06220.13150.04350.1076-61.387-22.38614.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 150
2X-RAY DIFFRACTION2B-1 - 150
3X-RAY DIFFRACTION3C-1 - 150
4X-RAY DIFFRACTION4D-1 - 150

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