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- PDB-6vde: Full-length M. smegmatis Pol1 -

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Basic information

Entry
Database: PDB / ID: 6vde
TitleFull-length M. smegmatis Pol1
ComponentsDNA polymerase I
KeywordsTRANSFERASE / mycobacteria / DNA polymerase / Flap endonuclease
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding
Similarity search - Function
DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 ...DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / DNA polymerase I / DNA polymerase I
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.713 Å
AuthorsShuman, S. / Goldgur, Y. / Ghosh, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30-CA008748 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Authors: Ghosh, S. / Goldgur, Y. / Shuman, S.
History
DepositionDec 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
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 I
B: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,3538
Polymers200,0232
Non-polymers3306
Water28816
1
A: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1764
Polymers100,0111
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1764
Polymers100,0111
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.004, 80.940, 117.912
Angle α, β, γ (deg.)98.680, 105.130, 109.360
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 18 - 908 / Label seq-ID: 18 - 908

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein DNA polymerase I


Mass: 100011.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: polA, MSMEI_3749
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I7G3P9, UniProt: A0QYZ2*PLUS, DNA-directed DNA polymerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M lithium chloride, 20% PEG6000, 0.1 M MES, 3% dextran sulfate sodium salt
Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 22, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50.5 Å / Num. obs: 60140 / % possible obs: 98.3 % / Redundancy: 4.5 % / CC1/2: 0.998 / Net I/σ(I): 24
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2877 / CC1/2: 0.662 / Rpim(I) all: 0.496

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6VDD

6vdd


Resolution: 2.713→50.366 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 39.56 / Details: 2877
RfactorNum. reflection% reflection
Rfree0.3042 1999 3.33 %
Rwork0.2344 --
obs0.2368 60059 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 322.58 Å2 / Biso mean: 117.8703 Å2 / Biso min: 51.35 Å2
Refinement stepCycle: final / Resolution: 2.713→50.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13344 0 6 16 13366
Biso mean--198.11 64.47 -
Num. residues----1720
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5238X-RAY DIFFRACTION4.013TORSIONAL
12B5238X-RAY DIFFRACTION4.013TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.713-2.78050.47391230.3857357284
2.7805-2.85570.38431400.3594405896
2.8557-2.93970.39321440.318417297
2.9397-3.03460.34721440.3106417498
3.0346-3.1430.39151420.3212416298
3.143-3.26890.39081440.3036416898
3.2689-3.41760.39631460.2762423599
3.4176-3.59770.36281450.2649421399
3.5977-3.82310.31431450.2488423299
3.8231-4.11810.28671470.2239423999
4.1181-4.53230.26951440.2086421299
4.5323-5.18760.2861450.2118419799
5.1876-6.53350.33141450.2508423099
6.5335-50.350.24571450.1847419698
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)
12.97450.63630.11354.0688-0.61823.94780.06540.5418-0.5302-0.33490.21620.53960.52-0.2562-0.21951.04960.0289-0.26410.80040.0121.161410.8693-18.10965.3659
22.1962-0.10471.1832.2226-0.48521.89980.18280.2093-0.2974-0.412-0.13150.08850.32140.1357-0.0540.7857-0.0124-0.01950.79230.05670.789319.42274.886412.5899
32.7078-0.00090.52232.71550.77713.9335-0.0280.4917-0.104-0.6938-0.505-0.1729-0.45220.71060.67391.4083-0.1617-0.0361.74080.34491.238831.704433.6102-8.0394
44.28450.6011-0.35392.9646-0.71723.8453-0.06820.65620.4271-0.5245-0.2496-0.1869-0.18880.860.3220.8047-0.0167-0.10511.02490.17850.803824.683724.075212.5985
54.7670.4262-0.70223.26720.39883.55850.0771-0.46830.58440.44770.1244-0.3264-0.82760.8498-0.17420.9774-0.1519-0.12751.0757-0.15150.863671.401443.822247.3905
63.40940.54450.86953.82341.21724.66240.2374-1.53140.20321.5618-0.3511-0.3759-0.28790.32910.19041.2551-0.1408-0.11961.2364-0.09120.809863.641235.515362.935
72.0954-0.70760.03123.19030.15373.1901-0.0072-1.03621.06291.54410.75960.5518-1.154-0.7059-0.58121.88150.16960.28361.5438-0.12661.433151.548444.440873.4082
83.86720.55450.11791.87240.1862.5225-0.06350.16980.3455-0.06910.0643-0.59140.090.58620.05381.0135-0.0644-0.13710.8605-0.01660.9870.35434.248135.1208
93.29870.8586-0.32864.0695-0.02473.1838-0.04630.06550.27430.3617-0.0029-0.001-0.0791-0.1273-0.04260.6263-0.0263-0.0390.65170.04850.762642.898126.631537.6264
103.84172.6727-0.20614.8552-2.10082.4308-0.06730.46420.02230.0988-0.0382-0.7245-0.04650.29570.0450.6748-0.0331-0.04890.81290.03520.789855.942627.78832.8906
110.85090.66250.79741.71050.13814.30790.2838-0.5422-0.2451.1699-0.2869-0.25210.52190.6231-0.0691.4435-0.118-0.09691.25050.18420.892247.409616.273570.1625
122.4339-0.26080.83112.4111-1.12342.11360.501-0.687-0.1008-0.0049-0.7383-0.58971.05250.59490.12381.95510.1488-0.21561.58890.20331.30946.5017-10.362667.6032
133.13720.43650.823.6594-0.3453.65890.4287-0.6555-0.52350.2698-0.20340.40821.227-0.2575-0.20171.4154-0.19280.04951.13310.21410.868435.5317.178957.827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 306 )A18 - 306
2X-RAY DIFFRACTION2chain 'A' and (resid 307 through 699 )A307 - 699
3X-RAY DIFFRACTION3chain 'A' and (resid 700 through 791 )A700 - 791
4X-RAY DIFFRACTION4chain 'A' and (resid 792 through 908 )A792 - 908
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 128 )B18 - 128
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 219 )B129 - 219
7X-RAY DIFFRACTION7chain 'B' and (resid 220 through 271 )B220 - 271
8X-RAY DIFFRACTION8chain 'B' and (resid 272 through 329 )B272 - 329
9X-RAY DIFFRACTION9chain 'B' and (resid 330 through 447 )B330 - 447
10X-RAY DIFFRACTION10chain 'B' and (resid 448 through 498 )B448 - 498
11X-RAY DIFFRACTION11chain 'B' and (resid 499 through 707 )B499 - 707
12X-RAY DIFFRACTION12chain 'B' and (resid 708 through 801 )B708 - 801
13X-RAY DIFFRACTION13chain 'B' and (resid 802 through 908 )B802 - 908

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