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- PDB-4dqq: Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A... -

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Basic information

Entry
Database: PDB / ID: 4dqq
TitleTernary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+
Components
  • DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / rCTP-dG / TRANSFERASE-DNA complex
Function / homology
Function and homology information


5'-3' exonuclease activity / 3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / 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 / Taq DNA Polymerase; Chain T, domain 4 ...: / DNA polymerase I, ribonuclease H-like domain / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease domain / 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 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.595 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
Authors: Wang, W. / Wu, E.Y. / Hellinga, H.W. / Beese, L.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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
A: DNA polymerase
D: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,06816
Polymers148,2176
Non-polymers1,85110
Water22,2121233
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1198
Polymers74,1093
Non-polymers1,0115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-36 kcal/mol
Surface area27330 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9498
Polymers74,1093
Non-polymers8405
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-57 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.540, 107.970, 149.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A, B, & C and chains D, E, & F).

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase


Mass: 67416.250 Da / Num. of mol.: 2 / Fragment: un residues 287-878 / Mutation: D598A, E658A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2635.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Primer Strand
#3: DNA chain DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4056.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Template Strand

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Non-polymers , 6 types, 1243 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1233 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE

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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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 58% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES (pH 5.8), VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.59→100 Å / Num. obs: 200705 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 29.023 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.59-1.690.4784.09192.3
1.69-1.810.277.261100
1.81-1.950.312.441100
1.95-2.140.1921.951100
2.14-2.390.10732.27199.9
2.39-2.760.06941.651100
2.76-3.380.04452.221100
3.38-4.780.03263.521100
4.78-1000.02669.65199.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1026refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2HVI

2hvi


Resolution: 1.595→79.354 Å / Occupancy max: 1 / Occupancy min: 0.02 / SU ML: 0.14 / σ(F): 2.35 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1794 8768 4.55 %
Rwork0.1601 --
obs0.161 192914 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7992 Å20 Å20 Å2
2--0.3805 Å2-0 Å2
3---0.4187 Å2
Refinement stepCycle: LAST / Resolution: 1.595→79.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9315 832 105 1233 11485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110718
X-RAY DIFFRACTIONf_angle_d1.35614708
X-RAY DIFFRACTIONf_dihedral_angle_d15.0984141
X-RAY DIFFRACTIONf_chiral_restr0.0731646
X-RAY DIFFRACTIONf_plane_restr0.0071760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5951-1.61330.2452570.23284889X-RAY DIFFRACTION77
1.6133-1.63230.25722950.21715597X-RAY DIFFRACTION89
1.6323-1.65220.25622970.215640X-RAY DIFFRACTION89
1.6522-1.67310.20183000.19945710X-RAY DIFFRACTION91
1.6731-1.69510.22663060.18925811X-RAY DIFFRACTION92
1.6951-1.71830.2023070.18895838X-RAY DIFFRACTION92
1.7183-1.74290.21853090.17855874X-RAY DIFFRACTION93
1.7429-1.76890.2223120.17715914X-RAY DIFFRACTION93
1.7689-1.79650.2033130.17465945X-RAY DIFFRACTION94
1.7965-1.8260.20423160.16676005X-RAY DIFFRACTION95
1.826-1.85750.20943170.1696040X-RAY DIFFRACTION96
1.8575-1.89120.18823160.16165994X-RAY DIFFRACTION95
1.8912-1.92760.19293240.15856157X-RAY DIFFRACTION97
1.9276-1.9670.19033220.15626120X-RAY DIFFRACTION96
1.967-2.00970.15372070.15736283X-RAY DIFFRACTION97
2.0097-2.05650.17952330.14926292X-RAY DIFFRACTION98
2.0565-2.10790.15972490.14816368X-RAY DIFFRACTION99
2.1079-2.16490.17222410.14946351X-RAY DIFFRACTION98
2.1649-2.22860.17662980.14726321X-RAY DIFFRACTION98
2.2286-2.30060.16212280.14436365X-RAY DIFFRACTION99
2.3006-2.38280.17842620.14646357X-RAY DIFFRACTION99
2.3828-2.47820.17372520.14446380X-RAY DIFFRACTION99
2.4782-2.5910.16212700.14946414X-RAY DIFFRACTION99
2.591-2.72760.17292740.15616399X-RAY DIFFRACTION99
2.7276-2.89850.17142940.16396406X-RAY DIFFRACTION99
2.8985-3.12230.18313140.16846458X-RAY DIFFRACTION100
3.1223-3.43650.15963400.15366414X-RAY DIFFRACTION100
3.4365-3.93380.17463290.14616515X-RAY DIFFRACTION100
3.9338-4.95610.14693390.13956526X-RAY DIFFRACTION100
4.9561-79.45220.20623470.1966763X-RAY DIFFRACTION100
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)
11.40790.2632-0.35282.6894-0.1571.4327-0.07480.1758-0.3302-0.1704-0.01010.05170.33160.01120.08280.24850.02120.02780.1426-0.02530.174119.5278-59.031325.3892
24.2981.7915-1.31072.4961-0.62842.0727-0.19860.65160.0303-0.38330.23850.30350.1008-0.2321-0.04370.25370.0024-0.04930.20590.00140.1689113.7174-51.176116.9273
30.44550.25850.13641.1277-0.55591.45440.0372-0.20510.0680.2790.01840.1003-0.04870.1985-0.05740.1933-0.03330.00480.0899-0.00710.1319117.0598-37.881546.7708
41.0046-1.11970.11392.9783-0.76141.0537-0.0431-0.18520.14130.37210.20080.4034-0.3276-0.111-0.1540.3538-0.00510.09940.1657-0.00760.2946103.9476-23.558848.818
51.50350.3764-0.19421.3831-0.04121.45320.0741-0.21730.07750.2615-0.0321-0.1232-0.01760.3538-0.03750.1603-0.0008-0.02420.1956-0.00750.113127.5835-32.120142.3188
61.8237-0.0920.37341.64510.14821.7805-0.0353-0.34540.40530.1092-0.0093-0.1455-0.40550.18550.03880.2162-0.06590.01840.2707-0.03060.238128.1807-13.656831.9015
70.89560.4811-0.31751.1061-0.10652.12830.0283-0.2406-0.07220.2513-0.1183-0.37390.08090.55940.08370.16540.0056-0.03680.30610.0210.1728133.4084-35.585440.7742
80.593-0.02480.14331.0862-0.13430.69480.00160.0760.0309-0.18180.0246-0.03350.01950.0035-0.0230.0917-0.01340.01540.1044-0.01920.0814129.1549-34.3054-19.1642
91.85321.0493-0.02281.8680.80430.94320.02930.51440.3935-0.4710.10360.0633-0.4458-0.1151-0.11180.23550.04080.02540.27390.06130.2521114.064-8.1647-9.1509
101.059-0.15820.01591.16350.44251.2290.01520.02160.2269-0.0292-0.04280.0681-0.1164-0.04450.02180.06910.01560.00020.09270.00560.1188119.5131-20.0579-5.0722
116.3551-0.7360.06661.7911-1.08572.3734-0.11860.07290.0287-0.41180.16480.4122-0.0278-0.1207-0.04060.2743-0.0451-0.03780.1151-0.02750.2653108.31-27.573139.7509
121.4422-0.0256-0.32061.3050.71411.34750.070.19930.6145-0.21210.16810.6542-0.2253-0.2633-0.24070.19810.01130.00560.16630.06510.3401109.4823-27.557437.59
133.61771.0863-2.26671.6666-0.41125.25890.02130.32030.4004-0.20910.192-0.49210.15340.0749-0.24540.20320.03540.04390.130.0030.2858129.4736-18.4229-27.0299
141.3763-0.7182-0.73190.7411-0.38491.99460.14420.12510.3561-0.460.283-0.5959-0.60330.3511-0.38140.2862-0.07970.13140.1956-0.010.2891130.8458-17.2012-23.7198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:409)
2X-RAY DIFFRACTION2chain 'A' and (resseq 410:467)
3X-RAY DIFFRACTION3chain 'A' and (resseq 468:522)
4X-RAY DIFFRACTION4chain 'A' and (resseq 523:604)
5X-RAY DIFFRACTION5chain 'A' and (resseq 605:676)
6X-RAY DIFFRACTION6chain 'A' and (resseq 677:780)
7X-RAY DIFFRACTION7chain 'A' and (resseq 781:876)
8X-RAY DIFFRACTION8chain 'D' and (resseq 293:646)
9X-RAY DIFFRACTION9chain 'D' and (resseq 647:728)
10X-RAY DIFFRACTION10chain 'D' and (resseq 729:876)
11X-RAY DIFFRACTION11chain 'B' and (resseq 21:29)
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:12)
13X-RAY DIFFRACTION13chain 'E' and (resseq 21:29)
14X-RAY DIFFRACTION14chain 'F' and (resseq 1:12)

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