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- PDB-2r9l: Polymerase Domain from Mycobacterium tuberculosis Ligase D in com... -

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Basic information

Entry
Database: PDB / ID: 2r9l
TitlePolymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA
Components
  • DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3')
  • DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3')
  • DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')
  • Putative DNA ligase-like protein
KeywordsTRANSFERASE/DNA / TRANSFERASE / PROTEIN-DNA COMPLEX / ATP-binding / Ligase / Nucleotide-binding / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


: / : / : / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication, synthesis of primer / double-strand break repair via nonhomologous end joining ...: / : / : / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication, synthesis of primer / double-strand break repair via nonhomologous end joining / DNA-directed RNA polymerase activity / 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 / DNA ligase D, polymerase domain / : / LigD, primase-polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA Ligase D 3'-phosphoesterase domain / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region ...Alpha-Beta Plaits - #3300 / LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / DNA ligase D, polymerase domain / : / LigD, primase-polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA Ligase D 3'-phosphoesterase domain / 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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Multifunctional non-homologous end joining DNA repair protein LigD / Multifunctional non-homologous end joining DNA repair protein LigD
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBrissett, N.C. / Fox, G.C. / Pitcher, R.S. / Doherty, A.J.
CitationJournal: Science / Year: 2007
Title: Structure of a NHEJ polymerase-mediated DNA synaptic complex
Authors: Brissett, N.C. / Pitcher, R.S. / Juarez, R. / Picher, A.J. / Green, A.J. / Dafforn, T.R. / Fox, G.C. / Blanco, L. / Doherty, A.J.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')
D: DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3')
E: DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')
F: DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3')
A: Putative DNA ligase-like protein
B: Putative DNA ligase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,44613
Polymers75,9676
Non-polymers4797
Water1,74797
1
C: DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')
D: DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3')
A: Putative DNA ligase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0298
Polymers37,6743
Non-polymers3545
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
MethodPISA
2
E: DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')
F: DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3')
B: Putative DNA ligase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4175
Polymers38,2933
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.531, 111.788, 139.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
12C
22E
13D
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALVALVAL1AE9 - 8112 - 84
211VALVALVALVAL1BF9 - 8112 - 84
321ALAALATHRTHR6AE82 - 8785 - 90
421ALAALATHRTHR6BF82 - 8785 - 90
531THRTHRVALVAL1AE88 - 11891 - 121
631THRTHRVALVAL1BF88 - 11891 - 121
741LEULEUPROPRO1AE126 - 140129 - 143
841LEULEUPROPRO1BF126 - 140129 - 143
951ALAALALEULEU1AE153 - 183156 - 186
1051ALAALALEULEU1BF153 - 183156 - 186
1161PROPROARGARG1AE186 - 202189 - 205
1261PROPROARGARG1BF186 - 202189 - 205
1371VALVALARGARG1AE226 - 255229 - 258
1471VALVALARGARG1BF226 - 255229 - 258
1581LEULEUALAALA5AE268 - 289271 - 292
1681LEULEUALAALA5BF268 - 289271 - 292
112DGDGDCDC1CA1 - 51 - 5
212DGDGDCDC1EC1 - 51 - 5
113DGDGDCDC4DB1 - 51 - 5
213DGDGDCDC4FD1 - 51 - 5

NCS ensembles :
ID
1
2
3

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Components

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DNA chain , 3 types, 4 molecules CEDF

#1: DNA chain DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')


Mass: 1521.024 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3')


Mass: 3328.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3')


Mass: 3946.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AB

#4: Protein Putative DNA ligase-like protein


Mass: 32825.148 Da / Num. of mol.: 2 / Fragment: LIGD polymerase domain residues 1-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Gene: Rv0938 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3)
References: UniProt: P71571, UniProt: P9WNV3*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 3 types, 104 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 52.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(w/v)PEG 3350, 0.2 M Ammonium chloride, 10mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium chloride11
2Ammonium chloride12
3MnCl211
4MnCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 29540 / % possible obs: 96.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Χ2: 0.856 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.496.50.39129380.801198.1
2.49-2.596.70.33529670.833199.2
2.59-2.770.25630010.838199.8
2.7-2.856.90.1930260.901199.9
2.85-3.026.90.13329960.949199.7
3.02-3.2670.0929830.993199.2
3.26-3.5870.06129830.88198.2
3.58-4.170.04629900.793197.5
4.1-5.166.80.03729020.714193.8
5.16-306.30.03727540.834184.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å21.13 Å
Translation2.5 Å21.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IRU

2iru


Resolution: 2.4→21.124 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.383 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1502 5.1 %RANDOM
Rwork0.227 ---
obs0.229 29486 96.78 %-
Solvent computationIon probe radii: 0.6 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 90.14 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å20 Å20 Å2
2---7.02 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 693 31 97 5169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225249
X-RAY DIFFRACTIONr_angle_refined_deg1.0152.1387286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14622.597181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5615695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4721542
X-RAY DIFFRACTIONr_chiral_restr0.0610.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023745
X-RAY DIFFRACTIONr_nbd_refined0.220.32297
X-RAY DIFFRACTIONr_nbtor_refined0.3220.53475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.5409
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4720.56
X-RAY DIFFRACTIONr_mcbond_it0.6811.52899
X-RAY DIFFRACTIONr_mcangle_it1.04824588
X-RAY DIFFRACTIONr_scbond_it1.57632910
X-RAY DIFFRACTIONr_scangle_it2.1734.52698
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1510TIGHT POSITIONAL0.030.05
1A88MEDIUM POSITIONAL0.260.5
1A132LOOSE POSITIONAL0.715
1A1510TIGHT THERMAL0.080.5
1A88MEDIUM THERMAL0.572
1A132LOOSE THERMAL210
2C105TIGHT POSITIONAL0.030.05
2C105TIGHT THERMAL0.050.5
3D98MEDIUM POSITIONAL0.250.5
3D98MEDIUM THERMAL0.512
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 124 -
Rwork0.287 2037 -
all-2161 -
obs--97.56 %
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)
12.9635-0.2897-0.85710.76381.36824.31180.0716-0.06580.51870.0992-0.1229-0.3499-0.63290.31370.0513-0.2939-0.0857-0.0813-0.24950.0049-0.329710.0339-11.8104-13.8771
25.96091.811-0.20710.03540.03523.4649-0.22770.6817-0.3046-1.21750.29450.7960.5779-0.0933-0.06690.1279-0.0944-0.3089-0.0889-0.0187-0.2107-17.4047-20.3539-56.5617
31.3065-2.7873.510618.9171-8.39089.49540.30160.21520.6349-0.6782-0.4069-0.7085-1.23420.83170.10540.3082-0.1003-0.0504-0.2158-0.0076-0.00878.99654.0545-18.4468
40.683-4.6216-0.327764.599813.34783.87450.25830.19720.448-0.8303-1.09661.6984-1.0556-0.51040.83830.4018-0.0438-0.3446-0.15840.06640.21281.73345.1346-20.8041
517.183-13.27797.692512.8025-4.12456.91180.72330.8576-1.9864-1.7531-0.6473-0.17370.92030.2769-0.0760.4412-0.0593-0.1236-0.1897-0.07210.3257-8.7992-34.6475-53.7896
65.657-4.049-4.133938.11322.82383.0213-0.2855-0.2589-0.37451.8461-0.3175-1.98010.78420.16910.6030.28310.0766-0.2915-0.1729-0.0201-0.1319-8.0872-29.1904-45.388
73.41830.72870.623512.77652.68072.6386-0.20770.29410.855-0.69790.21211.98240.0325-0.2765-0.0044-0.2437-0.0255-0.2965-0.18650.16350.1114-19.0044-1.5714-49.4339
810.66642.2682-2.340314.06311.49356.38350.198-0.47070.46320.3502-0.08632.2706-0.3526-0.0976-0.1117-0.26930.0169-0.0243-0.29270.07710.1387-17.31684.3106-42.1757
96.45382.47671.60178.98191.62033.21520.02910.02580.6531-0.1873-0.05252.60910.2535-0.69260.0234-0.2147-0.0614-0.2505-0.05690.09930.5706-27.4927-6.5164-48.446
103.3331.38712.11472.5695-0.92444.1559-0.3554-0.30610.5544-1.12570.03441.1889-0.4446-0.88710.3210.2260.0656-0.40050.06970.0309-0.036-3.8491-16.5133-31.8618
115.8902-0.99673.401314.5297.50488.12840.4052-0.89851.107-0.14770.24221.1699-0.2506-0.4867-0.64750.04390.0988-0.42620.11250.07770.1021-6.1885-12.1801-34.29
121.2545-0.27090.725311.03910.66832.86390.04590.0323-0.11410.0138-0.09220.679-0.0492-0.08320.0463-0.44360.0482-0.0557-0.2354-0.0098-0.38623.8224-30.1594-20.0025
138.91560.75420.01178.92310.69186.42380.40150.4766-0.5138-1.0823-0.19411.65010.0797-0.7813-0.2074-0.22150.0243-0.2244-0.1899-0.0417-0.0394-2.3721-35.2255-25.4391
142.29381.43410.327211.09622.76295.97780.1765-0.16150.01761.191-0.63981.01880.5004-0.50530.4633-0.3261-0.07060.113-0.1825-0.0689-0.30980.7795-28.1014-11.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE6 - 1049 - 107
2X-RAY DIFFRACTION2BF8 - 10411 - 107
3X-RAY DIFFRACTION3CA1 - 51 - 5
4X-RAY DIFFRACTION4DB1 - 51 - 5
5X-RAY DIFFRACTION5EC1 - 51 - 5
6X-RAY DIFFRACTION6FD1 - 71 - 7
7X-RAY DIFFRACTION7BF105 - 173108 - 176
8X-RAY DIFFRACTION8BF174 - 216177 - 219
9X-RAY DIFFRACTION9BF217 - 289220 - 292
10X-RAY DIFFRACTION10DB6 - 116 - 11
11X-RAY DIFFRACTION11FD8 - 138 - 13
12X-RAY DIFFRACTION12AE105 - 173108 - 176
13X-RAY DIFFRACTION13AE174 - 216177 - 219
14X-RAY DIFFRACTION14AE217 - 292220 - 295

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