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- PDB-6vdd: POL domain of Pol1 from M. smegmatis complex with DNA primer-temp... -

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Basic information

Entry
Database: PDB / ID: 6vdd
TitlePOL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3')
  • DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / mycobacteria / DNA polymerase / apoenzyme / TRANSFERASE-DNA complex
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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 ...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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 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 / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I / DNA polymerase I
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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 (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3')
C: DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
D: DNA polymerase I
E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3')
F: DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,92414
Polymers148,8766
Non-polymers1,0488
Water14,628812
1
A: DNA polymerase I
B: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3')
C: DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6658
Polymers74,1173
Non-polymers5485
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-55 kcal/mol
Surface area26860 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3')
F: DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2596
Polymers74,7593
Non-polymers5003
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-45 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.664, 233.805, 169.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase I


Mass: 66477.562 Da / Num. of mol.: 2 / Fragment: UNP residues 304-908
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

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DNA chain , 3 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3')


Mass: 3358.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 4280.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 4923.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 820 molecules

#5: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M magnesium chloride, 0.1 M MES, 25% PEG4000 / 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: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 24, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 104295 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 34.17 Å2 / CC1/2: 1 / Rpim(I) all: 0.033 / Net I/σ(I): 35.6
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5171 / CC1/2: 0.753 / Rpim(I) all: 0.414

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472+SVNrefinement
PHENIX1.15.2_3472+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→48.53 Å / SU ML: 0.1915 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3512
RfactorNum. reflection% reflection
Rfree0.2366 2000 1.92 %
Rwork0.1907 --
obs0.1916 104226 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8752 1025 6 812 10595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008610035
X-RAY DIFFRACTIONf_angle_d1.047513802
X-RAY DIFFRACTIONf_chiral_restr0.05411566
X-RAY DIFFRACTIONf_plane_restr0.00561637
X-RAY DIFFRACTIONf_dihedral_angle_d10.01775882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30371380.28837077X-RAY DIFFRACTION97.84
1.95-20.29271420.26477235X-RAY DIFFRACTION99.88
2-2.060.2661410.24567239X-RAY DIFFRACTION99.88
2.06-2.120.3041420.22817224X-RAY DIFFRACTION99.86
2.12-2.20.27041420.22547263X-RAY DIFFRACTION99.74
2.2-2.290.27751430.21737296X-RAY DIFFRACTION99.99
2.29-2.390.25721420.21187268X-RAY DIFFRACTION99.96
2.39-2.520.24051420.21567261X-RAY DIFFRACTION99.97
2.52-2.680.25721440.2197327X-RAY DIFFRACTION99.99
2.68-2.880.27061420.21727284X-RAY DIFFRACTION99.68
2.88-3.170.24671430.21167350X-RAY DIFFRACTION99.97
3.17-3.630.2491440.18497352X-RAY DIFFRACTION99.99
3.63-4.570.21111460.14947404X-RAY DIFFRACTION99.64
4.57-48.50.18971490.16057646X-RAY DIFFRACTION99.53
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)
13.319229167231.08685204926-0.7403816227522.041394051740.431262085493.217206910780.301375690755-0.180481965859-0.2006185872220.13416711197-0.0339960315480.1921970541770.446013898889-0.836493169499-0.2140965290670.300173572509-0.156954833369-0.09383313595570.4352048744540.1038295382940.274665284526-48.4157962187-52.7644985498-20.4384674745
21.24808114402-0.05805685831450.2797480492891.194487233130.02207984775880.942865837280.0479881059094-0.04616728355750.3404785972210.05197447576550.054846279239-0.0982105545737-0.298202553027-0.101019018983-0.09039965674490.264860008481-0.02408336586350.09971977726070.2285152224590.003043027486740.271329112403-36.1328142223-21.8227708562-17.6049369828
31.275815715410.2162672573940.6090240300331.028709656190.08728404574962.12385313346-0.1686761114810.214673658827-0.000432049342323-0.1922309975330.118213488037-0.367998847094-0.4953747930170.3354476044270.05372239047110.35019597344-0.1169555450750.07812855726850.255715123465-0.0361540555410.267193892714-17.4625424847-31.3683774267-20.5785631594
44.68211872076-2.219396986771.861633510113.99122902352-1.247040145455.4473807079-0.07361427295330.0732547374381-0.313590600016-0.04036503497750.1531173671420.574142312833-0.334076246319-0.820102457714-0.2007347119740.352164831294-0.02959849893390.0927680581940.421195480596-0.02297324892540.402530493312-39.4025033253-18.7963101698-25.1373371832
55.62137346598-1.1860080301-0.5284214568685.60558189783-0.07632283922132.563247403-0.2445699602280.535918672470.0964134745917-0.5065978297630.134029312720.49641405907-0.0796315655074-0.3776810939670.100372914610.403925770803-0.0476955665902-0.04030192733740.3669809050850.0100518644350.248154303642-39.4036318598-18.4166266207-27.4459542537
63.891422742881.4843145190.5309502481912.398023573030.2189273496912.483586659610.169431096382-0.07235076111740.246839161702-0.03299763093830.0575102256429-0.387327693313-0.2614932899330.550774702132-0.1700737734610.275010973049-0.1032309559220.1200733383510.36581990552-0.09540324363780.412825620586-16.5847823955-68.336683784-23.7833984772
72.10528500979-0.699664378423-0.894147426421.532693564580.4181062528090.932429590999-0.165608893869-0.0443968470247-0.4167437888010.08536305650830.03843111003830.1672212519240.2775193079680.08698441752640.09381781078120.303554015201-0.0625613373331-0.02806844452250.241331092302-0.02524754562680.293179545904-31.9610767034-100.531174678-15.8819805489
82.642405571360.454188183983-1.504155169792.904027246060.1282433428852.40334110321-0.503285139690.299809510773-0.193798467158-0.2247635279840.1987683062480.4082376854210.946943052188-0.2720402155290.3100173338230.692800538382-0.0942538339023-0.07146811675080.4137237618310.003644534309750.347956149313-52.4386225767-96.2955336553-28.530468546
92.36760493715-0.07097441809330.488433709211.525072447190.3482709545423.162779967140.054828456552-0.1854154119760.105336529932-0.04883980786540.03191470777710.1938452660640.0273049226606-0.117729438366-0.07766710148550.184411848778-0.04954462184430.005756856845820.204581005525-0.01537704584440.256098499813-40.3509435889-83.4344343947-11.638970501
105.97857362954-3.96064146807-1.991077936143.5433285791.92523201544.944144576950.03067263882780.6885094451060.684223764781-0.1446924644160.0432064902338-0.3459750025410.06716648045910.469664346206-0.04137093378170.353728883291-0.143801758432-0.05156747350160.4388662346250.02128365584510.453284912043-25.2791168035-102.180262964-26.0160836831
113.22525739701-1.100271600312.846007615836.91098021692-0.320084601424.92367162674-0.1525431857030.1970191786160.376828531617-0.9923990407780.155690075452-0.8590125633020.2144666849290.405948369798-0.04339607998090.48674507226-0.123444879060.1225905300620.355121522406-0.006854024387920.345149604556-24.0779607191-102.319145399-27.5544650904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 321 through 475 )
2X-RAY DIFFRACTION2chain 'A' and (resid 476 through 670 )
3X-RAY DIFFRACTION3chain 'A' and (resid 671 through 908 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'C' and (resid 7 through 20 )
6X-RAY DIFFRACTION6chain 'D' and (resid 322 through 498 )
7X-RAY DIFFRACTION7chain 'D' and (resid 499 through 707 )
8X-RAY DIFFRACTION8chain 'D' and (resid 708 through 811 )
9X-RAY DIFFRACTION9chain 'D' and (resid 812 through 908 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 11 )
11X-RAY DIFFRACTION11chain 'F' and (resid 8 through 20 )

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