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- PDB-3ne6: RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Oppos... -

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Basic information

Entry
Database: PDB / ID: 3ne6
TitleRB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG
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 / Mutation Frequencies / Kinetics / 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-templated 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 / : ...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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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: 2.001 Å
AuthorsWang, M. / Wang, J. / Konigsberg, W.H.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures.
Authors: Xia, S. / Wang, M. / Lee, H.R. / Sinha, A. / Blaha, G. / Christian, T. / Wang, J. / Konigsberg, W.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
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)114,6949
Polymers114,0263
Non-polymers6686
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-74 kcal/mol
Surface area43130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.135, 119.783, 130.652
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: 104533.023 Da / Num. of mol.: 1 / Mutation: D222A, D327A, S565G, Y567A
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(DE3) / 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, 763 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 7% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, 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: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 80207 / Num. obs: 79966 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 1.6 / Num. unique all: 7743 / % possible all: 97.8

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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 3NCI

3nci


Resolution: 2.001→49.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.253 / SU ML: 0.117 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.178 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22568 4009 5 %RANDOM
Rwork0.18352 ---
obs0.18562 75880 99.61 %-
all-76177 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.096 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å20 Å2
2--2.45 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.001→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7365 630 33 757 8785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228528
X-RAY DIFFRACTIONr_angle_refined_deg1.0552.05911722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0115981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21224.253395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.207151411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8591550
X-RAY DIFFRACTIONr_chiral_restr0.0730.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216368
X-RAY DIFFRACTIONr_mcbond_it1.22644631
X-RAY DIFFRACTIONr_mcangle_it2.09767555
X-RAY DIFFRACTIONr_scbond_it2.40763897
X-RAY DIFFRACTIONr_scangle_it3.59194129
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 253 -
Rwork0.258 5393 -
obs-5393 96.53 %
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)
10.0881-0.0509-0.12970.15670.11390.13240.05780.044-0.0233-0.0477-0.0177-0.10090.0061-0.0457-0.04010.12170.0114-0.03580.07310.00570.1258-16.89956.9629.55
20.06020.20350.05220.82590.20740.0894-0.0750.0579-0.1067-0.24850.1649-0.2813-0.00640.0648-0.08990.1469-0.03640.08250.0676-0.06380.21424.92862.11831.359
30.05450.07080.08170.66530.36920.3754-0.0294-0.0041-0.0188-0.1290.0845-0.1242-0.05110.0986-0.05520.0516-0.01410.02490.0554-0.02390.086510.43938.149.704
40.2524-0.0261-0.02910.6048-0.22840.17580.03850.13980.1164-0.11770.00670.08760.07960.0062-0.04530.1127-0.0032-0.0470.10420.05750.1242-3.65453.1254.802
50.56170.393-0.19521.3087-0.64620.4526-0.05040.17870.2709-0.01530.05540.07450.04690.0244-0.0050.1065-0.0359-0.06170.10770.09760.20149.28533.06617.867
60.2543-0.18220.08761.4017-0.43250.2677-0.0618-0.00120.0918-0.21240.1320.27940.063-0.0744-0.07010.1835-0.0195-0.1290.03470.0030.2587-9.54537.29117.8
71.2979-0.0713-0.22210.60970.0110.16990.19490.10061.13620.05380.06540.257-0.0454-0.1309-0.26030.19230.0130.29270.21520.12551.3387-22.11139.35337.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION2A1 - 105
4X-RAY DIFFRACTION2A340 - 389
5X-RAY DIFFRACTION3A106 - 339
6X-RAY DIFFRACTION4A390 - 468
7X-RAY DIFFRACTION4A576 - 706
8X-RAY DIFFRACTION5A469 - 575
9X-RAY DIFFRACTION6A707 - 737
10X-RAY DIFFRACTION7A738 - 901

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