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- PDB-4ki4: Ternary complex of rb69 mutant L415F with ribonucleotides at 0 an... -

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Basic information

Entry
Database: PDB / ID: 4ki4
TitleTernary complex of rb69 mutant L415F with ribonucleotides at 0 and -1 position
Components
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')
  • DNA polymerase
  • DNA/RNA (5'-D(*AP*C)-R(P*AP*G)-D(P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
KeywordsTRANSFERASE/DNA / RIBONUCLEOTIDE / 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 / : ...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 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 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/RNA hybrid / DNA/RNA hybrid (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsClausen, A.R. / Pedersen, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Authors: Clausen, A.R. / Murray, M.S. / Passer, A.R. / Pedersen, L.C. / Kunkel, T.A.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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/RNA (5'-D(*AP*C)-R(P*AP*G)-D(P*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*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,40115
Polymers114,5293
Non-polymers87312
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-109 kcal/mol
Surface area41760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.734, 118.840, 127.520
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 / DNA/RNA hybrid / DNA chain , 3 types, 3 molecules ATP

#1: Protein DNA polymerase / Gp43


Mass: 104689.156 Da / Num. of mol.: 1 / Mutation: D327A, D222A, L415F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: DNA/RNA hybrid DNA/RNA (5'-D(*AP*C)-R(P*AP*G)-D(P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5582.604 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')


Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 422 molecules

#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 MM TRIS-HCL, 16% PEG350, 180 MM CALCIUM CHLORIDE , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 45787 / Num. obs: 45787 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.523 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3CQ8

3cq8


Resolution: 2.45→38.485 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 2275 4.97 %
Rwork0.1917 --
obs0.1931 45787 99.15 %
all-45787 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→38.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7173 643 45 410 8271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028190
X-RAY DIFFRACTIONf_angle_d0.68511247
X-RAY DIFFRACTIONf_dihedral_angle_d11.2672745
X-RAY DIFFRACTIONf_chiral_restr0.0491201
X-RAY DIFFRACTIONf_plane_restr0.0031350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4431-2.49630.29151150.24732369X-RAY DIFFRACTION87
2.4963-2.55430.33491350.25422686X-RAY DIFFRACTION99
2.5543-2.61820.26531600.24342679X-RAY DIFFRACTION100
2.6182-2.6890.27911560.23732701X-RAY DIFFRACTION100
2.689-2.76810.29671400.23792712X-RAY DIFFRACTION100
2.7681-2.85740.26551440.23032706X-RAY DIFFRACTION100
2.8574-2.95950.24741340.22612738X-RAY DIFFRACTION100
2.9595-3.07790.28111430.22372701X-RAY DIFFRACTION100
3.0779-3.21790.26471240.21882755X-RAY DIFFRACTION100
3.2179-3.38750.21291510.21112710X-RAY DIFFRACTION100
3.3875-3.59960.24711370.19482749X-RAY DIFFRACTION100
3.5996-3.87730.23541550.1822728X-RAY DIFFRACTION100
3.8773-4.2670.16511480.15492763X-RAY DIFFRACTION100
4.267-4.88340.1651400.13762768X-RAY DIFFRACTION100
4.8834-6.14850.19111650.17232790X-RAY DIFFRACTION100
6.1485-38.48960.19131280.18442957X-RAY DIFFRACTION100
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)
10.78270.7254-0.34083.8187-1.29331.21840.10940.06020.24980.1773-0.1983-0.7098-0.10970.13480.10310.2271-0.00880.00460.33220.06680.718128.62561.141532.9948
20.990.2065-0.76823.01680.20652.10820.0116-0.15810.05420.6746-0.2041-0.32390.0013-0.00550.16890.3333-0.0134-0.1440.29030.01080.267313.431435.499854.4204
34.54891.00731.18452.55790.35391.61130.0811-0.43940.05970.1683-0.14130.12780.0475-0.28530.07370.23130.0285-0.00970.27820.03930.1922.995839.998341.1136
40.6224-0.12090.16611.8968-0.49881.02790.02920.06020.0999-0.1556-0.0806-0.16620.0997-0.02530.03740.1550.02470.02350.2248-0.01170.27.063645.734929.426
51.4524-0.04510.2492.1694-0.8071.37770.05830.36860.0116-0.7648-0.05-0.24410.48780.1462-0.03280.48810.08380.09060.34840.01880.17265.803845.082211.9047
61.78270.0633-0.20721.7-0.41061.3826-0.04160.0062-0.2639-0.26840.05950.35050.2048-0.1851-0.00120.2957-0.0029-0.08920.25430.02330.3185-16.064638.498223.619
79.64712.074-0.7031.29810.97121.5311-0.09510.2048-2.14530.1321-0.1701-0.29610.7439-0.21710.57510.4169-0.11570.0811.05370.13321.5082-37.243656.769630.6364
87.4162-2.93954.87445.7019-3.0439.5091-0.54371.21080.47330.14730.1487-0.7675-1.0038-0.08670.30380.37710.01040.02770.6710.15511.0089-23.22661.408729.7777
92.12630.1913-0.22132.0397-0.00062.42-0.03670.15270.2826-0.0537-0.1330.1562-0.0151-0.27330.12140.18060.0039-0.02270.2290.01020.2361-10.268949.620828.0502
107.3746-1.3016-2.7433.7988-2.81444.0687-0.2031-1.6750.62251.12250.4307-0.0438-0.739-0.3118-0.03580.39020.0789-0.01120.4235-0.08040.33634.274157.989329.8512
111.6079-0.095-0.15741.09340.55471.6689-0.2177-0.05010.46920.16050.19010.5522-0.0821-0.62410.06630.26450.10050.03380.39330.05080.4697-19.122554.984728.7578
124.7969-0.64490.30160.30260.77513.0849-0.98060.1739-0.05990.45010.0927-0.72650.00481.14180.31230.38490.0435-0.08030.55380.17361.3214-41.165765.403229.9573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:106)
2X-RAY DIFFRACTION2(chain A and resid 107:250)
3X-RAY DIFFRACTION3(chain A and resid 251:306)
4X-RAY DIFFRACTION4(chain A and resid 307:417)
5X-RAY DIFFRACTION5(chain A and resid 418:616)
6X-RAY DIFFRACTION6(chain A and resid 617:902)
7X-RAY DIFFRACTION7(chain P and resid 102:105)
8X-RAY DIFFRACTION8(chain P and resid 106:109)
9X-RAY DIFFRACTION9(chain P and resid 110:115)
10X-RAY DIFFRACTION10(chain T and resid 1:4)
11X-RAY DIFFRACTION11(chain T and resid 5:14)
12X-RAY DIFFRACTION12(chain T and resid 15:18)

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