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- PDB-6sa1: Post catalytic complex of Prim-PolC from Mycobacterium smegmatis ... -

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Basic information

Entry
Database: PDB / ID: 6sa1
TitlePost catalytic complex of Prim-PolC from Mycobacterium smegmatis with gapped DNA and 3'-dUTP
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*(DUI))-3')
  • DNA polymerase LigD, polymerase domain
KeywordsTRANSFERASE / Nucleotidyl transferase / Polymerase / Base excision repair / Protein-DNA complex
Function / homologyLigD, primase-polymerase domain / DNA ligase D, polymerase domain / metal ion binding / : / PYROPHOSPHATE / 3'-DEOXY-URIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase LigD, polymerase domain
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 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

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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*(DUI))-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*(DUI))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,23828
Polymers96,4718
Non-polymers1,76720
Water6,521362
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*(DUI))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,24614
Polymers48,2354
Non-polymers1,01110
Water362
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*(DUI))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,99214
Polymers48,2354
Non-polymers75610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.250, 198.250, 85.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain D and (resid 4 through 323 or (resid 324...
12chain C
22(chain F and resid 1 through 13)
13chain B
23chain E

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
111SERSERARGARGchain AAA4 - 3314 - 331
211SERSERPROPRO(chain D and (resid 4 through 323 or (resid 324...DE4 - 3234 - 323
221LYSLYSMETMET(chain D and (resid 4 through 323 or (resid 324...DE324 - 325324 - 325
231SERSERPROPRO(chain D and (resid 4 through 323 or (resid 324...DE4 - 3344 - 334
241SERSERPROPRO(chain D and (resid 4 through 323 or (resid 324...DE4 - 3344 - 334
251SERSERPROPRO(chain D and (resid 4 through 323 or (resid 324...DE4 - 3344 - 334
261SERSERPROPRO(chain D and (resid 4 through 323 or (resid 324...DE4 - 3344 - 334
112DCDCDADAchain CCC1 - 131 - 13
212DCDCDADA(chain F and resid 1 through 13)FG1 - 131 - 13
113DGDGDGDGchain BBB1 - 71 - 7
213DGDGDGDGchain EEF1 - 71 - 7

NCS ensembles :
ID
1
2
3

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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)
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*(DUI))-3')


Mass: 2115.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 382 molecules

#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-U3H / 3'-DEOXY-URIDINE 5'-TRIPHOSPHATE


Mass: 470.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N2O14P3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Sodium cacodylate, 2M Ammonium sulphate, 10mM Manganese Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2017 / Details: KB bimorph mirror pair
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.01→99.12 Å / Num. obs: 112811 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 44.314 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.01-2.045.61.23120755620.5941.423
5.46-99.25666.63642760490.0090.022

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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
DIALS1.7.3data reduction
xia20.5.438data scaling
PHASER2.7.17phasing
PHENIX1.12-2829refinement
Coot0.8.9.2model building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OP0

5op0


Resolution: 2.01→88.66 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2042 5636 5 %
Rwork0.1845 --
obs0.1855 112714 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 346.52 Å2 / Biso mean: 73.5611 Å2 / Biso min: 33.85 Å2
Refinement stepCycle: final / Resolution: 2.01→88.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 1099 173 362 6832
Biso mean--89 57.53 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096648
X-RAY DIFFRACTIONf_angle_d1.0169261
X-RAY DIFFRACTIONf_chiral_restr0.0591004
X-RAY DIFFRACTIONf_plane_restr0.0071022
X-RAY DIFFRACTIONf_dihedral_angle_d20.4583792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3202X-RAY DIFFRACTION8.175TORSIONAL
12D3202X-RAY DIFFRACTION8.175TORSIONAL
21C252X-RAY DIFFRACTION8.175TORSIONAL
22F252X-RAY DIFFRACTION8.175TORSIONAL
31B134X-RAY DIFFRACTION8.175TORSIONAL
32E134X-RAY DIFFRACTION8.175TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.03280.31641850.33113542100
2.0328-2.05680.29681990.29643474100
2.0568-2.08190.3131600.28393556100
2.0819-2.10820.2371760.27173533100
2.1082-2.13590.2862090.26033538100
2.1359-2.16520.27051860.25233466100
2.1652-2.19610.24681620.24513581100
2.1961-2.22890.24951770.23463543100
2.2289-2.26380.2541970.22833510100
2.2638-2.30090.24641880.21923540100
2.3009-2.34060.23661960.22113520100
2.3406-2.38310.24191720.20883555100
2.3831-2.4290.2191970.20843514100
2.429-2.47850.27361780.20843563100
2.4785-2.53240.25691870.19953532100
2.5324-2.59140.22971740.20043582100
2.5914-2.65620.23451910.20243548100
2.6562-2.7280.22181810.19953551100
2.728-2.80830.22451840.2053553100
2.8083-2.89890.25912020.21623535100
2.8989-3.00250.27582070.23313567100
3.0025-3.12270.22581760.21443579100
3.1227-3.26490.20741990.20783577100
3.2649-3.4370.24011850.19443596100
3.437-3.65240.1891680.18013610100
3.6524-3.93440.18072090.16453581100
3.9344-4.33030.17661770.1443648100
4.3303-4.95680.15371830.1363662100
4.9568-6.24490.18752060.15643680100
6.2449-88.660.16062250.1669384299
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)
11.8419-0.36731.172.04150.38124.2541-0.0527-0.1151-0.0881-0.0928-0.18290.45570.059-0.68540.2370.28780.00220.01090.5893-0.11470.4697-36.096-10.31776.5796
21.29-0.90531.1351.58250.31892.71040.009-0.0665-0.20130.0406-0.16610.43990.3639-0.45310.09740.3833-0.07290.05430.5244-0.06250.4711-29.5402-19.5738.2564
30.703-0.14820.13071.98061.86942.6774-0.2101-0.2304-0.0654-0.01070.06130.2754-0.0164-0.26030.03770.37860.08390.04410.4769-0.02350.4274-19.0136-16.168219.5615
40.93390.67270.68722.2481-0.09862.5164-0.1762-0.3039-0.00410.11040.05890.02190.0015-0.03410.12190.28180.10130.04090.4421-0.01780.3551-12.3378-10.113424.541
58.0229-2.6772-4.04576.27693.92623.4005-0.5132-0.9632-0.35030.99260.11130.34010.591-0.53020.5050.46880.12950.06660.68540.05360.356-19.6857-12.765536.148
60.54830.09120.48872.1965-0.81621.5331-0.1139-0.3345-0.02890.0558-0.00120.09760.2048-0.58140.16070.42670.02530.00670.5733-0.05680.3818-28.5453-9.878718.1502
71.6419-0.45560.3321.6842-0.37323.0092-0.09880.0220.171-0.1288-0.0856-0.056-0.1472-0.07680.20220.28050.04150.01160.3666-0.04530.3583-15.4524-3.896417.4533
88.24672.52934.99094.71042.85518.6278-0.28880.1739-1.67780.03350.41240.4341.7052-0.4523-0.00270.8252-0.0980.21850.73510.07050.7187-18.5037-27.561430.6904
92.4374.0323-0.33838.34851.66893.6084-0.0407-0.2092-1.3077-0.2040.2780.25521.6249-1.0725-0.23340.8627-0.3505-0.14520.9695-0.06441.3252-50.3867-25.76296.8279
102.60810.2177-3.45826.20271.85795.3801-0.0829-2.8244-0.99270.301-0.21170.72311.4616-0.80370.34690.9878-0.38150.17611.35170.14721.003-44.0303-25.647818.5117
113.27290.8303-2.77286.2943-1.99874.5391.98932.35323.35290.79130.70664.8931-1.58310.016-2.33191.5204-0.02720.61873.00310.80342.1213-41.9124-25.622430.9397
122.09241.1287-0.16012.51870.55112.8875-0.0625-0.14630.2053-0.0245-0.10080.4267-0.1817-0.51780.15280.41720.242-0.10540.704-0.14230.5112-45.455318.3624-2.6585
131.1832-0.30470.02880.85010.49121.50940.00520.03760.1177-0.2064-0.07590.2121-0.42-0.42870.03560.56960.247-0.12990.6006-0.10570.5153-35.753225.2489-11.7494
141.61290.4106-0.66731.4614-0.12532.0125-0.03340.1836-0.0362-0.2325-0.02740.1178-0.1471-0.2990.07570.44840.1781-0.11120.4433-0.11210.4131-28.895814.375-22.21
156.3186-1.803-3.42121.9791.44995.1349-0.1318-0.52511.2657-0.20730.22940.1648-1.3508-0.16490.22961.10120.3291-0.20810.8026-0.12770.7452-33.50833.2238-31.451
163.5062-1.7499-0.30694.53880.86780.1650.31460.34191.2677-0.0998-0.16770.4531-1.2398-0.9041-0.17931.00820.68550.09641.2273-0.17871.3154-60.02733.5788-2.7607
174.6830.8949-0.56473.06281.35123.3984-0.42391.92940.5204-0.5941-0.26271.4519-0.4016-0.60710.63761.44270.7449-0.23611.9171-0.0761.3941-56.210532.5469-17.7119
183.43452.4008-2.91043.31970.97468.04891.30291.43080.80660.2586-0.1612.4103-1.0735-0.2789-0.96352.04540.6534-0.54892.19880.50122.3565-56.127234.4077-27.9012
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 123 )A87 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 148 )A124 - 148
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 210 )A149 - 210
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 235 )A211 - 235
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 255 )A236 - 255
7X-RAY DIFFRACTION7chain 'A' and (resid 256 through 310 )A256 - 310
8X-RAY DIFFRACTION8chain 'A' and (resid 311 through 331 )A311 - 331
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 7 )B1 - 7
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 13 )C1 - 13
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 4 )H1 - 4
12X-RAY DIFFRACTION12chain 'D' and (resid 4 through 86 )D4 - 86
13X-RAY DIFFRACTION13chain 'D' and (resid 87 through 148 )D87 - 148
14X-RAY DIFFRACTION14chain 'D' and (resid 149 through 311 )D149 - 311
15X-RAY DIFFRACTION15chain 'D' and (resid 312 through 334 )D312 - 334
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 7 )E1 - 7
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 15 )F1 - 15
18X-RAY DIFFRACTION18chain 'G' and (resid 1 through 6 )G1 - 6

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