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- PDB-3snn: RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP... -

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Basic information

Entry
Database: PDB / ID: 3snn
TitleRB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dG in the presence of Mg2+
Components
  • 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'
  • 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 / DNA binding / 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 / 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-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 Å
AuthorsWang, M. / Wang, J. / Konigsberg, W.H.
CitationJournal: Biochemistry / Year: 2011
Title: Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.
Authors: Xia, S. / Wang, M. / Blaha, G. / Konigsberg, W.H. / Wang, J.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Sep 13, 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.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_seq_id / _struct_conn.ptnr2_label_asym_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
T: 5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'
P: 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4566
Polymers113,9403
Non-polymers5163
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-37 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.327, 119.525, 130.740
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 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
#2: DNA chain 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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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase / Gp43


Mass: 104446.938 Da / Num. of mol.: 1 / Mutation: D222A, D327A, L561A, 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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Non-polymers , 3 types, 588 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 52.38 %
Crystal growTemperature: 293.15 K / Method: microbatch vapor diffusion / pH: 6.5
Details: 150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, soak crystals with the same buffer containing 100 mM magnesium chloride instead of calcium chloride, MICROBATCH ...Details: 150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, soak crystals with the same buffer containing 100 mM magnesium chloride instead of calcium chloride, MICROBATCH VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 80808 / Num. obs: 79354 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.25 / Num. unique all: 7959 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IG9

1ig9


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.892 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.183 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22243 3961 5 %RANDOM
Rwork0.19324 ---
obs0.1947 74966 98.18 %-
all-76356 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2---0.12 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 630 30 585 8604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228328
X-RAY DIFFRACTIONr_angle_refined_deg1.0652.06111400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37224.127378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.485151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0261548
X-RAY DIFFRACTIONr_chiral_restr0.0720.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216164
X-RAY DIFFRACTIONr_mcbond_it1.07344532
X-RAY DIFFRACTIONr_mcangle_it1.87467353
X-RAY DIFFRACTIONr_scbond_it2.22763796
X-RAY DIFFRACTIONr_scangle_it3.32894040
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 311 -
Rwork0.297 5514 -
obs--99.2 %
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)
11.4193-0.3653-0.03930.31610.04850.0337-0.1452-0.04230.0826-0.05490.07360.1140.003-0.01820.07160.09410.0173-0.0230.14580.01250.174-17.11757.05429.726
20.3932-0.0499-0.0581.9537-0.56470.68960.01830.00490.04910.0278-0.0494-0.162-0.04360.09290.0310.0512-0.01440.0010.10770.00260.122625.00762.13431.598
30.50030.13240.06471.0462-0.07141.24560.0153-0.03870.00950.1366-0.02940.00020.0674-0.07080.0140.06940.0002-0.01160.0910.00140.075510.27937.9750.161
40.71480.5011-0.10051.1724-0.02570.4711-0.01950.18810.0051-0.18770.0696-0.00220.0182-0.0759-0.05020.1109-0.0104-0.0110.13540.01590.0512-3.5553.1775.025
50.53070.3855-0.01654.36060.48460.4493-0.03360.0238-0.12840.0357-0.0219-0.03070.0910.01550.05560.08670.00570.01280.10780.00290.07579.49433.48518.059
61.721-0.4131-1.42720.83690.74432.6332-0.05990.0733-0.0683-0.04740.05560.0390.08490.03430.00420.0954-0.0347-0.02270.10680.00360.0958-9.48337.17217.441
71.3505-0.06380.26290.94320.37162.5109-0.0646-0.1821-0.10640.09690.07930.17760.0717-0.1763-0.01480.01540.02190.02790.08670.06470.1031-22.3239.27637.526
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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