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- PDB-6sa0: Ternary complex of Prim-PolC from Mycobacterium smegmatis with 2n... -

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Basic information

Entry
Database: PDB / ID: 6sa0
TitleTernary complex of Prim-PolC from Mycobacterium smegmatis with 2nt gapped DNA and UpNHpp
Components
  • DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')
  • DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')
  • DNA (5'-D(P*TP*GP*CP*GP)-3')
  • DNA polymerase LigD, polymerase domain
KeywordsTRANSFERASE / Nucleotidyl transferase / Polymerase / Base excision repair / Protein-DNA complex
Function / homology
Function and homology information


DNA ligase D, polymerase domain / : / LigD, primase-polymerase domain
Similarity search - Domain/homology
Chem-2KH / CACODYLATE ION / : / DNA / DNA (> 10) / DNA polymerase LigD, polymerase domain
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.209 Å
AuthorsBrissett, N.C. / Doherty, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/F013795/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J018643/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M004236/1 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C.
Authors: Brissett, N.C. / Zabrady, K. / Plocinski, P. / Bianchi, J. / Korycka-Machala, M. / Brzostek, A. / Dziadek, J. / Doherty, A.J.
History
DepositionJul 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase LigD, polymerase domain
B: DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')
H: DNA (5'-D(P*TP*GP*CP*GP)-3')
D: DNA polymerase LigD, polymerase domain
E: DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')
G: DNA (5'-D(P*TP*GP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,40018
Polymers95,8908
Non-polymers1,50910
Water8,251458
1
A: DNA polymerase LigD, polymerase domain
B: DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')
H: DNA (5'-D(P*TP*GP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,79910
Polymers47,9454
Non-polymers8546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA polymerase LigD, polymerase domain
E: DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')
G: DNA (5'-D(P*TP*GP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6008
Polymers47,9454
Non-polymers6554
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.059, 136.059, 133.479
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 178 or resid 180 through 336))
21(chain D and (resid 4 through 178 or resid 180...
12chain C
22chain F
13chain B
23chain E
14chain G
24chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLY(chain A and (resid 4 through 178 or resid 180 through 336))AA4 - 1784 - 178
121GLYGLYLYSLYS(chain A and (resid 4 through 178 or resid 180 through 336))AA180 - 336180 - 336
211SERSERGLYGLY(chain D and (resid 4 through 178 or resid 180...DE4 - 1784 - 178
221GLYGLYSERSER(chain D and (resid 4 through 178 or resid 180...DE180 - 335180 - 335
231LYSLYSLYSLYS(chain D and (resid 4 through 178 or resid 180...DE336336
241SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
251SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
261SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
271SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
281SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
291SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
2101SERSERLYSLYS(chain D and (resid 4 through 178 or resid 180...DE4 - 3364 - 336
112DCDCDGDGchain CCC1 - 151 - 15
212DCDCDGDGchain FFG1 - 151 - 15
113DGDGDGDGchain BBB1 - 71 - 7
213DGDGDGDGchain EEF1 - 71 - 7
114DCDCDGDGchain GGH1 - 61 - 6
214DCDCDGDGchain HHD1 - 61 - 6

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase LigD, polymerase domain


Mass: 39416.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: ligD / Variant: ATCC 700084 / mc(2)155 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R5T1

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DNA chain , 3 types, 6 molecules BECFHG

#2: DNA chain DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')


Mass: 2163.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')


Mass: 4539.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*GP*CP*GP)-3')


Mass: 1825.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 468 molecules

#5: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Sodium cacodylate, 2M Ammonium Chloride, 10mM Manganese Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2017 / Details: KB bimorph mirror pair
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.208→117.83 Å / Num. obs: 71872 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 34.136 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.21-2.256.51.52280135180.5951.53899
5.99-118618.22291738150.0230.056100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.03 Å99.12 Å
Translation3.03 Å99.12 Å

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Processing

Software
NameVersionClassification
DIALS1.5.0data reduction
xia20.5.270data scaling
PHASER2.7.17phasing
PHENIX1.12-2829refinement
PDB_EXTRACT3.25data extraction
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OP0

5op0


Resolution: 2.209→58.071 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.2065 3502 4.93 %
Rwork0.1745 --
obs0.1761 71066 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.48 Å2 / Biso mean: 51.0788 Å2 / Biso min: 23.58 Å2
Refinement stepCycle: final / Resolution: 2.209→58.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5267 1140 103 458 6968
Biso mean--59.46 50.41 -
Num. residues----722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136772
X-RAY DIFFRACTIONf_angle_d1.3099465
X-RAY DIFFRACTIONf_chiral_restr0.0671027
X-RAY DIFFRACTIONf_plane_restr0.0081040
X-RAY DIFFRACTIONf_dihedral_angle_d19.7193877
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3249X-RAY DIFFRACTION7.064TORSIONAL
12D3249X-RAY DIFFRACTION7.064TORSIONAL
21C292X-RAY DIFFRACTION7.064TORSIONAL
22F292X-RAY DIFFRACTION7.064TORSIONAL
31B134X-RAY DIFFRACTION7.064TORSIONAL
32E134X-RAY DIFFRACTION7.064TORSIONAL
41G112X-RAY DIFFRACTION7.064TORSIONAL
42H112X-RAY DIFFRACTION7.064TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.209-2.23880.31971330.3133263797
2.2388-2.27080.35081130.2965270498
2.2708-2.30470.3161540.2934260898
2.3047-2.34070.32871640.2889264398
2.3407-2.37910.32831730.277261998
2.3791-2.42010.30481250.2671268199
2.4201-2.46410.31231170.2591268698
2.4641-2.51150.29841350.2412269498
2.5115-2.56270.32431450.2468267599
2.5627-2.61850.27511590.2264264999
2.6185-2.67940.28421420.2282267999
2.6794-2.74640.22551400.2137267599
2.7464-2.82060.24771280.2065270299
2.8206-2.90360.26661300.199269899
2.9036-2.99730.25881250.2059270499
2.9973-3.10450.23931570.1979269599
3.1045-3.22880.24821460.18262721100
3.2288-3.37570.18711200.1725270999
3.3757-3.55360.20591580.1573272499
3.5536-3.77620.19121200.1511273699
3.7762-4.06770.16491160.1354276199
4.0677-4.4770.14431400.1148272999
4.477-5.12450.14061780.11632736100
5.1245-6.45490.16761380.13932798100
6.4549-58.0710.12671460.1509290199
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)
10.67730.1023-0.06742.6167-0.60290.15640.35190.03010.27750.2573-0.09040.1582-0.609-0.1066-0.14460.85520.130.33640.35610.07730.5286-33.964628.467420.1491
26.87625.41170.83164.26880.73170.5316-0.23010.51080.7459-0.89110.26360.4911-0.3503-0.2406-0.08410.81880.24270.08450.45660.16330.6172-42.511118.97547.4028
30.86990.0463-0.19272.3042-0.47090.91370.21120.08430.0245-0.0301-0.01980.1046-0.2051-0.1166-0.15840.43340.11350.10190.27730.05580.3081-35.06314.900820.8048
41.8590.2426-0.35315.0368-0.21422.69860.2878-0.22440.12050.3079-0.106-0.7388-0.43150.5131-0.08780.546-0.03680.08020.38950.04130.4669-20.691112.834927.733
52.87760.4916-0.22551.72940.41821.04440.19580.2628-0.0996-0.2179-0.06930.14050.0662-0.1666-0.13410.47880.1364-0.0110.37020.06660.3232-41.5044-3.626215.0383
62.5051-0.84111.07620.3797-0.12321.0453-0.3870.03630.4972-0.299-0.34180.8182-0.4252-0.24550.26161.20450.69890.37340.21060.16561.2986-51.417941.176217.083
70.26210.09730.34372.1251-0.21150.54190.2512-0.08850.7188-0.1537-0.27110.5402-0.5066-0.50860.41440.75710.37060.21010.4850.06041.087-54.564925.039420.345
85.76950.4552.37252.5711-1.24422.8408-0.1366-0.82110.7535-0.164-0.05310.4835-0.2798-0.89410.09310.3890.1578-0.01610.6267-0.02420.4632-56.97266.400128.0169
91.97190.1752-0.72712.2609-1.01874.239-0.10940.0746-0.4396-0.09420.24740.45790.7116-0.9217-0.06630.3607-0.1069-0.01650.78480.10390.555-40.683111.7945-17.4897
102.13280.4945-0.15632.84830.47043.5298-0.04210.0276-0.1870.05640.04590.16920.3536-0.3014-0.06320.2694-0.0080.06370.55230.09750.3865-29.506817.1917-16.7561
111.72280.9639-0.02172.4526-0.12330.4660.0672-0.0910.19140.28360.16170.6446-0.0323-0.4354-0.07860.34060.10720.12610.76670.08230.4953-36.904228.8095-11.1806
121.46270.72930.38461.7936-0.17430.8049-0.08410.0551-0.04810.06970.1220.0261-0.0008-0.1316-0.04010.24710.10170.05210.53890.02560.2829-15.664629.9356-15.9656
131.94651.27820.40764.76650.03061.5210.0441-0.2261-0.30960.71530.0933-0.27050.16850.0618-0.13840.260.12420.04210.4660.00210.3056-10.464725.9837-7.5521
142.84711.6356-1.41543.0451-0.51550.9246-0.2209-0.01810.44320.03260.10550.2377-0.3777-0.120.00220.35190.14360.00060.51440.00510.3659-17.518750.6228-15.3377
152.693-0.40171.26330.0576-0.18270.5915-0.4475-0.36090.5521-0.0173-0.04840.6214-0.4285-0.6809-0.07160.28290.062-0.02151.1985-0.06641.1868-55.641426.009-17.4505
163.65871.45450.81410.63980.61781.666-0.1649-0.2401-0.0774-0.2507-0.11940.9065-0.074-0.71970.18860.32610.1504-0.02960.8784-0.00020.9952-42.976437.2522-19.9873
173.5693-1.2299-0.50070.45340.11330.22980.0840.12150.0743-0.6995-0.53190.6128-0.3542-0.26880.31620.48170.2522-0.14520.6174-0.05390.5139-27.238348.7334-26.2686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 86 )A4 - 86
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 106 )A87 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 255 )A107 - 255
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 286 )A256 - 286
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 336 )A287 - 336
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 7 )B1 - 7
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 15 )C1 - 15
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 6 )H1 - 6
9X-RAY DIFFRACTION9chain 'D' and (resid 4 through 26 )D4 - 26
10X-RAY DIFFRACTION10chain 'D' and (resid 27 through 63 )D27 - 63
11X-RAY DIFFRACTION11chain 'D' and (resid 64 through 106 )D64 - 106
12X-RAY DIFFRACTION12chain 'D' and (resid 107 through 276 )D107 - 276
13X-RAY DIFFRACTION13chain 'D' and (resid 277 through 310 )D277 - 310
14X-RAY DIFFRACTION14chain 'D' and (resid 311 through 336 )D311 - 336
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 7 )E1 - 7
16X-RAY DIFFRACTION16chain 'F' and (resid 1 through 15 )F1 - 15
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 6 )G1 - 6

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