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- PDB-3nci: RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 ... -

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Basic information

Entry
Database: PDB / ID: 3nci
TitleRB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution
Components
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
  • DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / RB69 DNA polymerase / fidelity / base selectivity / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWang, M. / Blaha, G. / Steitz, T.A. / Konigsberg, W.H. / Wang, J.
CitationJournal: Biochemistry / Year: 2011
Title: Insights into base selectivity from the 1.8 A resolution structure of an RB69 DNA polymerase ternary complex.
Authors: Wang, M. / Xia, S. / Blaha, G. / Steitz, T.A. / Konigsberg, W.H. / Wang, J.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
P: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7367
Polymers114,1483
Non-polymers5874
Water24,7351373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-54 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.504, 119.404, 129.763
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 / / Gp43


Mass: 104655.141 Da / Num. of mol.: 1 / Fragment: DNA polymerase / Mutation: D222A, D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

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


Mass: 5541.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA strand
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA strand

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Non-polymers , 3 types, 1377 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1373 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: micro-batch vapor-diffusion / pH: 6.5
Details: 8%(w/v) PEG 350 monomethyl ether (MME),160 mM CaCl2, and 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9095 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2009 / Details: mirrors
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9095 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 104627 / Num. obs: 99370 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 0.86 / Num. unique all: 8061 / % possible all: 74

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IG9

1ig9


Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.855 / SU ML: 0.08 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20136 5207 5 %RANDOM
Rwork0.17474 ---
obs0.17607 99370 94.28 %-
all-105399 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7374 630 31 1373 9408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228520
X-RAY DIFFRACTIONr_angle_refined_deg1.0052.05911710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8635977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21924.278395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.024151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2871549
X-RAY DIFFRACTIONr_chiral_restr0.0680.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216359
X-RAY DIFFRACTIONr_mcbond_it0.9144623
X-RAY DIFFRACTIONr_mcangle_it1.6667542
X-RAY DIFFRACTIONr_scbond_it1.90763897
X-RAY DIFFRACTIONr_scangle_it2.98794131
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 291 -
Rwork0.365 4857 -
obs-4857 63.41 %
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)
10.27690.06470.02650.052-0.00270.0161-0.10130.01050.1085-0.01550.0660.0446-0.0054-0.02360.03540.05190.0116-0.02040.11680.01230.1177-16.89956.9629.55
20.11290.1493-0.09451.2783-0.44420.38650.00980.00920.04050.0505-0.0398-0.099-0.01790.06650.030.0044-0.0041-0.00690.05850.00170.064824.92862.11831.359
30.30450.21650.05170.7350.02570.68480.0231-0.02070.01070.1123-0.0381-0.01070.0438-0.04920.0150.0225-0.0061-0.0060.0551-0.00270.010510.43938.149.704
40.66220.5009-0.18091.0224-0.0580.2451-0.06590.1960.0339-0.19470.10470.02480.008-0.0831-0.03880.0586-0.0276-0.0160.12280.02550.0134-3.65453.1254.802
50.31220.16770.03422.65970.29330.2212-0.04840.0581-0.0730.00210.0299-0.05340.06380.03770.01850.0355-0.00030.01840.0659-0.01070.0239.28533.06617.867
61.0051-0.0945-0.36020.41710.13320.7226-0.04990.0738-0.0760.00710.02470.01360.0654-0.03710.02510.037-0.0275-0.00180.0536-0.00180.0365-9.54537.29117.8
71.13370.09350.35190.63430.32951.3706-0.0783-0.1767-0.06990.05980.10480.10160.0092-0.1342-0.02650.01340.02630.02140.08170.04480.0527-22.11139.35337.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A904
4X-RAY DIFFRACTION2A1 - 105
5X-RAY DIFFRACTION2A340 - 389
6X-RAY DIFFRACTION3A106 - 339
7X-RAY DIFFRACTION4A390 - 468
8X-RAY DIFFRACTION4A576 - 706
9X-RAY DIFFRACTION5A469 - 575
10X-RAY DIFFRACTION6A707 - 737
11X-RAY DIFFRACTION7A738 - 901

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