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- PDB-3f2b: DNA Polymerase PolC from Geobacillus kaustophilus complex with DN... -

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Basic information

Entry
Database: PDB / ID: 3f2b
TitleDNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn
Components
  • 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3'
  • 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3'
  • DNA-directed DNA polymerase III alpha chain
KeywordsTRANSFERASE/DNA / DNA Polymerase C / DNA Polymerase III / Ternary Complex / Protein-DNA complex / Replicative DNA Polymerase / DNA replication / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
PolC, middle finger domain / DNA polymerase; domain 1 - #870 / glyoxalase-related enzyme like fold - #20 / Helix Hairpins - #1510 / Insulin-like, subunit E - #10 / DNA polymerase III PolC-like, N-terminal domain II / DNA polymerase III PolC-type, N-terminal domain I / PolC, middle finger subdomain superfamily / DNA polymerase III polC-type N-terminus II / DNA polymerase III polC-type N-terminus I ...PolC, middle finger domain / DNA polymerase; domain 1 - #870 / glyoxalase-related enzyme like fold - #20 / Helix Hairpins - #1510 / Insulin-like, subunit E - #10 / DNA polymerase III PolC-like, N-terminal domain II / DNA polymerase III PolC-type, N-terminal domain I / PolC, middle finger subdomain superfamily / DNA polymerase III polC-type N-terminus II / DNA polymerase III polC-type N-terminus I / glyoxalase-related enzyme like fold / Insulin-like, subunit E / DNA polymerase III, alpha subunit, Gram-positive type / DNA polymerase III epsilon subunit, exonuclease domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Helix Hairpins / Metal-dependent hydrolases / Nucleic acid-binding proteins / Helix non-globular / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleic acid-binding, OB-fold / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase III PolC-type
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsDavies, D.R. / Evans, R.J. / Bullard, J.M. / Christensen, J. / Green, L.S. / Guiles, J.W. / Ribble, W.K. / Janjic, N. / Jarvis, T.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of PolC reveals unique DNA binding and fidelity determinants.
Authors: Evans, R.J. / Davies, D.R. / Bullard, J.M. / Christensen, J. / Green, L.S. / Guiles, J.W. / Pata, J.D. / Ribble, W.K. / Janjic, N. / Jarvis, T.C.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Dec 27, 2023Group: 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 / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_conn.ptnr2_label_seq_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-directed DNA polymerase III alpha chain
P: 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3'
T: 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,12911
Polymers129,1983
Non-polymers9308
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-73 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.174, 140.793, 184.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA-directed DNA polymerase III alpha chain


Mass: 117248.508 Da / Num. of mol.: 1 / Fragment: GKAPOLC, DELTA 1-227, DELTA 412-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: GK1258, polC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L0J3, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3'


Mass: 5246.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer strand synthetic oligonucleotide
#3: DNA chain 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3'


Mass: 6703.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template strand synthetic oligonucleotide

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Non-polymers , 5 types, 103 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 20% PEG 2000 MME, 0.1M PHOSPHATE- CITRATE, 200MM LITHIUM SULFATE, PH 5.3, VAPOR DIFFUSION, pH 5.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000 MME11
2PHOSPHATE- CITRATE11
3LITHIUM SULFATE11
4PEG 2000 MME12
5PHOSPHATE- CITRATE12
6LITHIUM SULFATE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 / Wavelength: 0.999887 Å
DetectorDetector: CCD / Date: Apr 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
20.9998871
ReflectionResolution: 2.4→43.52 Å / Num. obs: 59793 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.824 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.39→43.52 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.074 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3017 5.1 %RANDOM
Rwork0.228 ---
obs0.231 59703 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--2.29 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.39→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7815 631 50 95 8591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228731
X-RAY DIFFRACTIONr_angle_refined_deg1.6092.06811954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32624.254362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.471151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4951547
X-RAY DIFFRACTIONr_chiral_restr0.1080.21334
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216347
X-RAY DIFFRACTIONr_mcbond_it0.5121.54945
X-RAY DIFFRACTIONr_mcangle_it0.98128003
X-RAY DIFFRACTIONr_scbond_it1.59333786
X-RAY DIFFRACTIONr_scangle_it2.5534.53951
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 209 -
Rwork0.406 3979 -
obs--95.95 %
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)
16.2547-2.1881.82143.4847-2.22233.31640.1029-0.0269-0.1923-0.2610.15080.19990.22610.0005-0.2536-0.0716-0.04590.0062-0.07590.0776-0.126738.2807-12.1426-16.1455
20.86180.5266-0.37951.91220.00432.2246-0.1189-0.0029-0.1036-0.15610.3534-0.11640.5792-0.3697-0.23450.1107-0.1935-0.0693-0.03370.0333-0.103138.594.3948-46.4176
31.205-0.13270.2083.01020.59673.2898-0.09540.32970.1666-0.36850.23050.21980.3546-1.0761-0.1351-0.0555-0.3262-0.12190.33520.1301-0.17528.132712.3487-57.2261
40.541-0.0845-1.93411.21860.94727.2598-0.28860.5237-0.1452-0.27670.34940.1930.8801-1.6472-0.06080.1967-0.5306-0.1490.39660.1297-0.046923.9795-1.6722-49.0967
50.82720.83580.38591.70820.38171.5743-0.15120.1995-0.1771-0.32760.4086-0.40380.5009-0.3021-0.25740.1489-0.269-0.0292-0.01120.0007-0.154238.99521.051-53.3966
61.33840.36360.30330.7591-0.19832.54410.13050.02190.09240.0496-0.0135-0.0852-0.49340.2139-0.117-0.0145-0.00950.0457-0.0955-0.008-0.017655.699544.7092-25.8983
70.2318-0.04480.04870.7185-0.1130.29910.0030.00790.09320.00140.20340.14820.0118-0.2095-0.2064-0.10420.0172-0.00110.05730.0789-0.022834.478524.5086-31.5013
81.5735-0.4002-0.27950.3185-0.09261.27770.0315-0.11520.0230.08550.0522-0.06930.09640.083-0.0837-0.06170.0342-0.0175-0.0439-0.0093-0.055151.578928.5676-9.9096
92.8411-2.6449-0.67124.5791-0.56031.46980.0434-0.2805-0.36320.09510.00850.20560.2194-0.3591-0.052-0.06340.05210.0170.0290.0786-0.062925.616730.3168-1.0801
107.811-1.84160.65140.4371-0.16310.08560.09080.40820.1689-0.1412-0.18220.0009-0.0908-0.06050.0915-0.04010.1150.05310.09970.0218-0.07299.021545.177-12.4536
111.5170.50470.40310.89530.96151.0484-0.15040.02270.12390.0688-0.13060.3199-0.0795-0.47960.281-0.09270.03970.04580.20760.01850.108423.630724.2914-19.8596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A233 - 331
2X-RAY DIFFRACTION2A332 - 411
3X-RAY DIFFRACTION3A619 - 708
4X-RAY DIFFRACTION4A716 - 772
5X-RAY DIFFRACTION5A773 - 825
6X-RAY DIFFRACTION6A826 - 996
7X-RAY DIFFRACTION7A997 - 1122
8X-RAY DIFFRACTION8A1123 - 1307
9X-RAY DIFFRACTION9A1308 - 1359
10X-RAY DIFFRACTION10A1360 - 1444
11X-RAY DIFFRACTION11P5 - 17
12X-RAY DIFFRACTION11T1 - 18

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