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- PDB-3f2c: DNA Polymerase PolC from Geobacillus kaustophilus complex with DN... -

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Basic information

Entry
Database: PDB / ID: 3f2c
TitleDNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP and Mn
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'
  • GEOBACILLUS KAUSTOPHILUS DNA POLC
KeywordsTRANSFERASE/DNA / DNA Polymerase C / DNA Polymerase III / Ternary Complex / Protein-DNA complex / Replicative polymerase / gram-positive / 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 / : / DNA / DNA (> 10) / DNA polymerase III PolC-type
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Sep 6, 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.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: GEOBACILLUS KAUSTOPHILUS DNA POLC
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)130,0329
Polymers129,1983
Non-polymers8336
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-72 kcal/mol
Surface area45170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.889, 141.185, 184.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GEOBACILLUS KAUSTOPHILUS DNA POLC


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) / 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 is 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 is synthetic oligonucleotide

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Non-polymers , 5 types, 161 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 155 / 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: 57.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 20% PEG 2000 MME, 0.1M PHOSPHATE CITRATE, 200MM LITHIUM SULFATE, 2 mM MnCl2, 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
4MnCl211
5PHOSPHATE CITRATE12
6LITHIUM SULFATE12
7PEG 2000 MME12
8MnCl212

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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: 2.5→43.6 Å / Num. obs: 51829 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.589 / % possible all: 91.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F2B

3f2b


Resolution: 2.5→43.6 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 17.736 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.413 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2641 5.1 %RANDOM
Rwork0.21 ---
obs0.213 51791 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--2.62 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7796 631 40 155 8622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228704
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4522.06711920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35124.294361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.096151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8621546
X-RAY DIFFRACTIONr_chiral_restr0.0940.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216338
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3911.54940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77227993
X-RAY DIFFRACTIONr_scbond_it1.25933764
X-RAY DIFFRACTIONr_scangle_it2.0794.53927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 166 -
Rwork0.323 3189 -
obs--87.28 %
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)
16.93971.8614-1.68343.4265-2.20344.35380.0477-0.13720.04710.19470.1070.226-0.37880.0223-0.1547-0.09390.03820.0149-0.12440.0636-0.15738.208411.986716.2396
20.5268-0.29960.62612.5295-0.1013.074-0.1605-0.030.17170.1650.3536-0.0528-0.6574-0.4296-0.19310.04770.19020.0805-0.04350.0066-0.11638.3642-4.475346.4072
31.7111-0.012-0.77493.64820.28082.8538-0.0727-0.2165-0.11410.440.24420.3224-0.3418-1.0216-0.1716-0.09140.31220.11070.28180.105-0.194827.8924-12.428157.116
40.60960.1771.58941.0290.40398.2219-0.2881-0.50170.08210.37590.50050.2951-0.824-1.7698-0.21240.14470.5460.15610.33690.1148-0.092123.63641.418848.9645
50.7698-1.0055-0.1542.7929-0.40052.3983-0.2083-0.32670.16790.50980.5394-0.3862-0.7219-0.4012-0.3310.10360.2770.0434-0.01550.0064-0.191938.6683-1.178353.3823
61.4144-0.2406-0.23271.293-0.12872.81990.0890.0163-0.1739-0.0492-0.032-0.12850.56380.1901-0.0569-0.0101-0.0006-0.034-0.1509-0.004-0.051255.6121-44.676825.9865
70.24280.02220.01150.7389-0.10670.37340.0188-0.0146-0.0782-0.01850.16870.14990.0546-0.2712-0.1875-0.1116-0.01960.01690.04990.0554-0.068334.3961-24.537831.5109
81.94590.65350.53080.5855-0.13641.2568-0.00050.1668-0.008-0.14060.0461-0.0466-0.06990.082-0.0456-0.0558-0.04080.0233-0.078-0.0159-0.094451.4769-28.60959.8977
94.67772.34031.50585.359-1.06523.8951-0.03770.34780.5815-0.1575-0.01060.448-0.3113-0.41350.0483-0.0996-0.0641-0.0104-0.01480.0757-0.093125.5823-30.38551.1107
108.07542.7721-1.21530.9586-0.39090.28210.0988-0.476-0.2170.2034-0.187-0.0248-0.0115-0.02720.0882-0.0503-0.1044-0.02740.05330.0172-0.08669.0143-45.274212.4399
111.6546-0.808-0.48131.26051.27041.378-0.1848-0.0209-0.1744-0.12-0.19990.48120.3065-0.51380.3847-0.1237-0.0816-0.04850.1708-0.00620.144723.5739-24.458519.952
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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