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- PDB-3cfp: Structure of the replicating complex of a POL Alpha family DNA Po... -

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Entry
Database: PDB / ID: 3cfp
TitleStructure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 1
Components
  • DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3')
  • DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*(DOC))-3')
  • DNA polymerase
KeywordsTransferase/DNA / DNA POLYMERASE / CATALYTIC COMPLEX / FIDELITY / TWO METAL ION MECHANISM / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / Transferase-DNA COMPLEX
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesBacteriophage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, J. / Klimenko, D. / Wang, M. / Steitz, T.A. / Konigsberg, W.H.
Citation
Journal: To be Published
Title: Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant
Authors: Klimenko, D. / Wang, M. / Steitz, T.A. / Konigsberg, W.H. / Wang, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure of a POL Alpha family replicative DNA Polymerase from bacteriophage RB69
Authors: Wang, J. / Sattar, A.K. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A. / Franklin, M.C.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of the replicating complex of a POL Alpha DNA polymerase
Authors: Franklin, M.C. / Wang, J. / Steitz, T.A.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3')
P: DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*(DOC))-3')
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8779
Polymers115,1993
Non-polymers6786
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-72.3 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.726, 117.281, 126.813
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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DNA chain , 2 types, 2 molecules TP

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


Mass: 5550.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHEsized by W.M. KECK FACILITY AT YALE UNIVERSITY)
#2: DNA chain DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*(DOC))-3')


Mass: 4240.768 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHEsized by W.M. KECK FACILITY AT YALE UNIVERSITY)

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase / / Gp43


Mass: 105407.852 Da / Num. of mol.: 1 / Mutation: L561A, S565G, Y567A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase

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Non-polymers , 4 types, 305 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% PEG350 monomethyl ether, 0.1M NA CACODYLATE, 0.14M CACL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1NA CACODYLATE11
2CaCl211
3NA CACODYLATE12
4PEG350 monomethyl ether12
5CaCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDetector: CCD / Date: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42496 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.5→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.1045 / Num. unique all: 9961

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 25.497 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26662 2074 4.9 %RANDOM
Rwork0.1969 ---
obs0.20047 39995 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2---2.21 Å20 Å2
3---3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 650 34 299 8326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2922.06611330
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57224.167372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.012151342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.541546
X-RAY DIFFRACTIONr_chiral_restr0.0860.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026106
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.23983
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25619
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2560.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.73124612
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.77637286
X-RAY DIFFRACTIONr_scbond_it1.66624429
X-RAY DIFFRACTIONr_scangle_it2.55734044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 130 -
Rwork0.317 2759 -
obs--94.47 %
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)
15.6862-0.6942-0.36822.2342-0.19880.0515-0.1797-0.13320.3602-0.05520.11560.620.0670.01570.064-0.11990.0194-0.03620.03960.03110.1837-19.27555.83528.297
20.83150.65170.01083.4686-0.89491.14180.06840.04320.12110.0712-0.0236-0.9269-0.07470.0479-0.0448-0.20890.00390.0399-0.1173-0.00470.412625.06958.830.556
30.85730.3688-0.58263.12350.0770.9860.03020.0075-0.07460.5844-0.0096-0.40790.0221-0.07-0.0206-0.00330.0171-0.1846-0.09450.01440.00819.38235.3650.629
42.050.6339-0.10162.4698-0.26050.52620.0270.59410.1681-0.65920.04330.0110.1047-0.0728-0.07030.0828-0.00340.01110.07890.0696-0.1968-3.34748.9823.734
50.87550.66550.29216.2023-0.20840.61890.12010.1618-0.1326-0.402-0.0353-0.38050.29390.0568-0.08480.03610.03990.0355-0.053-0.0147-0.0118.91129.76618.048
62.3471-0.9239-0.8261.1328-1.26063.56020.03280.102-0.0578-0.31820.02330.1370.1167-0.0986-0.0561-0.0262-0.0911-0.0463-0.053-0.04610.0169-10.00833.83416.848
71.5015-0.39870.33392.4701-0.5352.3196-0.1772-0.2169-0.35250.39970.33330.6051-0.145-0.3164-0.1561-0.13060.05660.1368-0.0440.1160.0812-2337.96836.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1TA1 - 181 - 18
2X-RAY DIFFRACTION1PB102 - 1151 - 14
4X-RAY DIFFRACTION2AC1 - 1051 - 105
5X-RAY DIFFRACTION2AC340 - 389340 - 389
6X-RAY DIFFRACTION3AC106 - 339106 - 339
7X-RAY DIFFRACTION4AC390 - 468390 - 468
8X-RAY DIFFRACTION4AC576 - 706576 - 706
9X-RAY DIFFRACTION5AC469 - 575469 - 575
10X-RAY DIFFRACTION6AC707 - 737707 - 737
11X-RAY DIFFRACTION7AC738 - 901738 - 901

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