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- PDB-4mky: Polymerase Domain from Mycobacterium tuberculosis Ligase D in com... -

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Basic information

Entry
Database: PDB / ID: 4mky
TitlePolymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.
Components
  • 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
  • 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
  • DNA ligase-like protein Rv0938/MT0965
KeywordsTRANSFERASE/DNA / protein-DNA complex / transferase-DNA complex / Nucleotide-binding / polymerase / primase / transferase
Function / homology
Function and homology information


: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / single-stranded DNA 3'-5' DNA exonuclease activity / DNA primase activity / DNA replication, synthesis of primer / DNA-directed 5'-3' RNA polymerase activity ...: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / single-stranded DNA 3'-5' DNA exonuclease activity / DNA primase activity / DNA replication, synthesis of primer / DNA-directed 5'-3' RNA polymerase activity / double-strand break repair via nonhomologous end joining / double-strand break repair / manganese ion binding / DNA recombination / DNA-directed DNA polymerase activity / nucleotide binding / magnesium ion binding / DNA binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #3300 / LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. ...Alpha-Beta Plaits - #3300 / LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Multifunctional non-homologous end joining DNA repair protein LigD / Multifunctional non-homologous end joining DNA repair protein LigD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBrissett, N.C. / Doherty, A.J.
CitationJournal: Cell Rep / Year: 2013
Title: Molecular Basis for DNA Double-Strand Break Annealing and Primer Extension by an NHEJ DNA Polymerase.
Authors: Brissett, N.C. / Martin, M.J. / Bartlett, E.J. / Bianchi, J. / Blanco, L. / Doherty, A.J.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase-like protein Rv0938/MT0965
B: DNA ligase-like protein Rv0938/MT0965
C: DNA ligase-like protein Rv0938/MT0965
D: DNA ligase-like protein Rv0938/MT0965
E: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
G: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
I: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
K: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
F: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
H: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
J: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
L: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)149,50512
Polymers149,50512
Non-polymers00
Water3,531196
1
A: DNA ligase-like protein Rv0938/MT0965
B: DNA ligase-like protein Rv0938/MT0965
E: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
G: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
F: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
H: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)74,7526
Polymers74,7526
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-31 kcal/mol
Surface area27240 Å2
MethodPISA
2
C: DNA ligase-like protein Rv0938/MT0965
D: DNA ligase-like protein Rv0938/MT0965
I: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
K: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
J: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
L: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)74,7526
Polymers74,7526
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-29 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.580, 80.110, 118.390
Angle α, β, γ (deg.)90.00, 111.62, 90.00
Int Tables number4
Space group name H-MP1211
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: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA10 - 29110 - 291
21BB10 - 29110 - 291
12AA10 - 29310 - 293
22CC10 - 29310 - 293
13AA10 - 29310 - 293
23DD10 - 29310 - 293
14BB10 - 29110 - 291
24CC10 - 29110 - 291
15BB10 - 29110 - 291
25DD10 - 29110 - 291
16CC10 - 29310 - 293
26DD10 - 29310 - 293

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
DNA ligase-like protein Rv0938/MT0965


Mass: 32825.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0965, MTCY08D9.01c, MTCY10D7.36c, Rv0938 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: P71571, UniProt: P9WNV3*PLUS
#2: DNA chain
5'-D(P*DGP*DCP*DGP*DGP*DC)-3'


Mass: 1521.024 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SYNTHESISED DNA
#3: DNA chain
5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'


Mass: 3029.994 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SYNTHESISED DNA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200mM Ammonium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 10, 2009 / Details: mirrors
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.71
11H, -K, -H-L20.29
ReflectionResolution: 2.4→110.061 Å / Num. all: 58964 / Num. obs: 58964 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rsym value: 0.117 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.4-2.536.40.8250.90.825196.1
2.53-2.686.30.6191.20.619196.5
2.68-2.876.20.4241.80.424197.9
2.87-3.16.20.2842.70.284199
3.1-3.396.40.1475.20.147199.8
3.39-3.796.80.1087.10.108199.9
3.79-4.387.30.06910.80.0691100
4.38-5.377.40.0514.10.051100
5.37-7.597.30.05313.20.0531100
7.59-46.0087.10.03216.90.032199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.5 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.64 Å
Translation2.5 Å37.64 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IRU

2iru


Resolution: 2.4→37.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.616 / SU ML: 0.14 / SU R Cruickshank DPI: 0.0781 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24529 2951 5 %RANDOM
Rwork0.19734 ---
obs0.19969 55990 98.1 %-
Solvent computationIon probe radii: 0.6 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.065 Å2
Baniso -1Baniso -2Baniso -3
1-19.02 Å20 Å2-6.55 Å2
2--40.65 Å20 Å2
3----59.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8680 1060 0 196 9936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01810064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.86213945
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16451131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83722.617363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1281584
X-RAY DIFFRACTIONr_chiral_restr0.0810.21555
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0217308
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9082.2664536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43.8175663
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1132.3285528
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A3300.25
12B3300.25
21A3370.26
22C3370.26
31A3470.25
32D3470.25
41B3310.27
42C3310.27
51B3270.25
52D3270.25
61C3360.26
62D3360.26
LS refinement shellResolution: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 202 -
Rwork0.277 3833 -
obs--91.04 %
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)
11.59530.10930.41561.2905-0.10961.97750.0189-0.201-0.08180.2235-0.0815-0.18350.01380.26340.06260.1402-0.00720.06060.11020.04620.352127.5717-41.187133.1511
22.00540.1022-0.31641.21610.20861.93530.0194-0.38870.08910.29340.0070.08760.0345-0.2653-0.02640.2525-0.00960.06470.2566-0.02040.4161-12.0887-40.553832.8619
32.44420.08120.26511.3960.08981.7237-0.0974-0.3663-0.15350.29690.0649-0.1774-0.14280.09140.03250.23030.05890.07090.12130.03260.403855.87530.948711.1152
41.2289-0.0818-0.40021.49380.02222.04020.05220.02570.06610.0707-0.02790.02040.0026-0.077-0.02430.0718-0.00940.07030.00530.0060.312616.1990.025211.3345
520.1476-2.23718.66920.2867-0.430711.37360.12130.0697-0.2318-0.0103-0.01120.0443-0.12460.2525-0.11010.5097-0.0340.05520.4146-0.1010.4352-12.1378-40.904358.3955
617.0722-0.6219-2.23940.3194-1.15735.4752-0.0121-0.09310.10860.0811-0.0899-0.0478-0.32890.3580.1020.3339-0.0254-0.05080.34090.0970.410527.3907-38.159358.4494
72.84555.16581.302310.54333.5442.01480.0906-0.4967-0.17320.135-0.3484-0.4049-0.0290.34910.25770.57940.0113-0.10110.54130.11210.656155.88492.940636.6194
827.786-15.63841.911512.9684-1.83580.27440.2846-0.6051-0.42311.492-0.13531.2924-0.27780.0544-0.14940.6862-0.16780.39880.2141-0.13750.370916.5642-2.535336.5655
95.16030.5971-3.89760.3093-1.42587.28710.1082-0.2404-0.58350.0002-0.0272-0.04650.06230.0391-0.0810.58990.00860.00480.47640.05160.55691.1053-41.157249.886
103.00871.94982.34611.77312.44923.5540.09870.00340.48330.0756-0.24470.25620.1343-0.40840.14610.59120.0113-0.00480.3384-0.01830.490714.201-38.881149.755
112.81211.86031.68581.82351.91892.1086-0.0536-0.08730.34660.0374-0.05970.22180.0268-0.03590.11330.57070.01950.12060.51220.01390.528442.55341.947328.0542
124.38332.2592-2.35742.1441-2.59383.21460.02010.131-0.7644-0.0215-0.1932-0.26360.05360.27740.1730.49320.0723-0.00150.29540.01810.45829.7413-1.741427.7984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 446
2X-RAY DIFFRACTION2B10 - 292
3X-RAY DIFFRACTION3C10 - 440
4X-RAY DIFFRACTION4D10 - 456
5X-RAY DIFFRACTION5E1 - 3
6X-RAY DIFFRACTION6G1 - 101
7X-RAY DIFFRACTION7I1 - 3
8X-RAY DIFFRACTION8K1 - 102
9X-RAY DIFFRACTION9F1 - 107
10X-RAY DIFFRACTION10H1 - 107
11X-RAY DIFFRACTION11J1 - 105
12X-RAY DIFFRACTION12L1 - 107

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