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- PDB-4e0d: Binary complex of Bacillus DNA Polymerase I Large Fragment E658A ... -

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Basic information

Entry
Database: PDB / ID: 4e0d
TitleBinary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA
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 / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 5, 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 / struct_conn / struct_ref_seq / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
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)75,60613
Polymers74,1093
Non-polymers1,49710
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-108 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.860, 93.780, 104.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase


Mass: 67416.250 Da / Num. of mol.: 1
Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment)
Mutation: D598A, E658A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK2730, GYMC61_0787, polA / 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, 2 molecules BC

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


Mass: 2635.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer Strand / Source: (synth.) Synthetic construct (others)
#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.: 1 / Source method: obtained synthetically / Details: Template Strand / Source: (synth.) Synthetic construct (others)

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Non-polymers , 5 types, 834 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: 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
#7: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 47% 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: 1.1159 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: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.58→100 Å / Num. obs: 117529 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 26.883 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.58-1.670.4764.33198.9
1.67-1.790.357.53199.4
1.79-1.930.31512.69197
1.93-2.120.15920.6199.1
2.12-2.370.10427.03196.9
2.37-2.730.06339.31100
2.73-3.350.04347.871100
3.35-4.730.03258.21199.6
4.73-1000.02668.54199.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1026refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DQQ chains A, B, and C

4dqq


Resolution: 1.58→54.703 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.12 / σ(F): 2.35 / Phase error: 16.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 5646 5 %
Rwork0.1611 --
obs0.1621 112902 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1404 Å2-0 Å2-0 Å2
2---1.9461 Å20 Å2
3----3.1943 Å2
Refinement stepCycle: LAST / Resolution: 1.58→54.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 365 89 824 5917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015284
X-RAY DIFFRACTIONf_angle_d1.3357248
X-RAY DIFFRACTIONf_dihedral_angle_d15.6552052
X-RAY DIFFRACTIONf_chiral_restr0.07812
X-RAY DIFFRACTIONf_plane_restr0.007865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.5980.20531690.20633210X-RAY DIFFRACTION87
1.598-1.61680.24641750.20043319X-RAY DIFFRACTION89
1.6168-1.63650.21381780.19093384X-RAY DIFFRACTION91
1.6365-1.65720.22641790.18673408X-RAY DIFFRACTION91
1.6572-1.6790.22231790.18483392X-RAY DIFFRACTION92
1.679-1.7020.20071840.17193493X-RAY DIFFRACTION94
1.702-1.72630.19341830.17023478X-RAY DIFFRACTION93
1.7263-1.75210.20531840.16473500X-RAY DIFFRACTION94
1.7521-1.77950.18521870.16813552X-RAY DIFFRACTION95
1.7795-1.80860.181880.16663576X-RAY DIFFRACTION95
1.8086-1.83980.20991870.15933554X-RAY DIFFRACTION96
1.8398-1.87330.1821860.16563536X-RAY DIFFRACTION94
1.8733-1.90930.2251580.19352991X-RAY DIFFRACTION80
1.9093-1.94830.28761730.24923282X-RAY DIFFRACTION88
1.9483-1.99070.18431880.16073590X-RAY DIFFRACTION96
1.9907-2.0370.18631950.15243692X-RAY DIFFRACTION98
2.037-2.08790.16671930.14643676X-RAY DIFFRACTION99
2.0879-2.14440.17691960.14623728X-RAY DIFFRACTION99
2.1444-2.20750.1761940.14863670X-RAY DIFFRACTION98
2.2075-2.27870.2331680.20073207X-RAY DIFFRACTION85
2.2787-2.36020.15621930.14333654X-RAY DIFFRACTION97
2.3602-2.45470.15311970.13843755X-RAY DIFFRACTION99
2.4547-2.56640.18791980.14753761X-RAY DIFFRACTION100
2.5664-2.70170.18141990.15423771X-RAY DIFFRACTION100
2.7017-2.87090.19371980.15813768X-RAY DIFFRACTION100
2.8709-3.09260.20412000.16213801X-RAY DIFFRACTION100
3.0926-3.40380.17092010.15323814X-RAY DIFFRACTION100
3.4038-3.89620.15142000.13953802X-RAY DIFFRACTION99
3.8962-4.90830.1462040.13443872X-RAY DIFFRACTION100
4.9083-54.73590.17852120.1964020X-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)
11.4288-0.7516-0.27951.4205-0.02351.0029-0.1025-0.2028-0.07210.15480.0970.06170.06810.0123-0.01010.09140.01840.01160.12130.00860.0979-9.6396-20.870546.8369
20.44-0.04950.28540.5005-0.04471.32710.0147-0.04630.036-0.1521-0.02630.13610.0763-0.40860.01710.1417-0.0212-0.0180.1818-0.00260.1514-31.0496-6.921918.7379
30.5327-0.0251-0.00880.4253-0.21810.61530.0220.0519-0.018-0.1022-0.00330.07310.04390.0023-0.00830.10520.0067-0.01430.0912-0.00530.125-7.768-1.963316.7774
44.74450.4775-0.1142.857-0.00773.77090.0741-0.3479-0.5255-0.3167-0.14210.22670.7568-0.20510.10980.2993-0.0075-0.05570.23230.02980.2396-25.8073-14.15216.8944
55.38282.36531.94112.28870.1341.3661-0.06580.4312-0.136-0.3440.1695-0.02561.0513-0.2678-0.0880.384-0.0957-0.02870.2967-0.01380.2315-25.9484-14.925620.1541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:467)
2X-RAY DIFFRACTION2chain 'A' and (resseq 468:604)
3X-RAY DIFFRACTION3chain 'A' and (resseq 605:876)
4X-RAY DIFFRACTION4chain 'B' and (resseq 21:29)
5X-RAY DIFFRACTION5chain 'C' and (resseq 4:12)

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