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- PDB-3si6: RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Com... -

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Basic information

Entry
Database: PDB / ID: 3si6
TitleRB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mg2+
Components
  • 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3'
  • 5'-D(*TP*CP*AP*AP*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 / : ...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'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 17, 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.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_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*AP*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*C)-3'
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4325
Polymers113,9403
Non-polymers4912
Water20,0691114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-35 kcal/mol
Surface area43310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.458, 120.195, 131.205
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*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'


Mass: 5525.592 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*C)-3'


Mass: 3967.585 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: pET 21b / 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, 1116 molecules

#4: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 52.89 %
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, MICROBATCH VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→44.314 Å / Num. all: 102120 / Num. obs: 100690 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.25 / Num. unique all: 9956 / % possible all: 99

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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: 1.85→44.314 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.136 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21685 5010 5 %RANDOM
Rwork0.18279 ---
all0.18451 97495 --
obs0.18451 95428 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å20 Å2
2--0.45 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 630 29 1114 9132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0228289
X-RAY DIFFRACTIONr_angle_refined_deg0.8512.06211341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6225906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70324.133375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.243151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6541547
X-RAY DIFFRACTIONr_chiral_restr0.060.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216122
X-RAY DIFFRACTIONr_mcbond_it0.92944511
X-RAY DIFFRACTIONr_mcangle_it1.68967311
X-RAY DIFFRACTIONr_scbond_it1.94563778
X-RAY DIFFRACTIONr_scangle_it2.97794028
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 336 -
Rwork0.265 6486 -
obs--90.89 %
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)
10.2767-0.110.04410.13450.00870.026-0.07770.01210.05650.00150.02330.0911-0.0135-0.0290.05450.0960.0085-0.00570.18010.02310.1925-17.24357.29229.82
20.3490.0478-0.07831.3286-0.39480.54370.00830.01880.07370.0647-0.0234-0.1663-0.05210.06220.01510.0323-0.0080.00030.08430.00580.128825.10762.6131.709
30.34840.1603-0.04331.01390.09621.12250.0126-0.03850.01840.1833-0.0188-0.02380.1014-0.04460.00610.070.0034-0.0140.08050.00070.05310.41938.12950.53
40.79770.4223-0.20661.0511-0.06170.4347-0.02930.27570.0136-0.21720.09660.0246-0.0054-0.1221-0.06720.0789-0.0059-0.01340.16740.02830.0288-3.44153.3624.815
50.51140.1873-0.08143.18560.38390.4711-0.04610.0893-0.11740.01740.0062-0.1010.1198-0.00250.03980.0674-0.00080.01070.1081-0.00930.06739.57133.75218.145
60.70070.2042-0.36970.5157-0.00690.8771-0.07790.0318-0.1187-0.00720.05930.0410.04350.03570.01860.0673-0.0241-0.00970.1247-0.00540.0962-9.27337.1717.049
71.290.01920.28170.80.29091.7739-0.0736-0.1859-0.14340.090.09490.15390.0063-0.1525-0.02130.01480.02430.0290.10920.07120.1127-22.45639.43837.441
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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