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- PDB-4ki6: Ternary complex of rb69 mutant l415f with ribonucleotides at -1 a... -

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Basic information

Entry
Database: PDB / ID: 4ki6
TitleTernary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 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*CP*A)-R(P*GP*G)-D(P*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
PHOSPHATE ION / 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: 2.55 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*CP*A)-R(P*GP*G)-D(P*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)115,39213
Polymers114,5293
Non-polymers86410
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-127 kcal/mol
Surface area41370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.853, 118.400, 127.970
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*CP*A)-R(P*GP*G)-D(P*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5582.605 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, 179 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.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 MM TRIS-HCL, 16% PEG350, 180 MM CALCIUM CHLORIDE, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 39756 / Num. obs: 39756 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.4
Reflection shellResolution: 2.55→2.59 Å / % possible all: 86.2

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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: 3CQ8

3cq8


Resolution: 2.55→35.947 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1994 5.02 %
Rwork0.1953 --
obs0.1972 39755 97.41 %
all-39756 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→35.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7098 652 42 169 7961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028051
X-RAY DIFFRACTIONf_angle_d0.65211075
X-RAY DIFFRACTIONf_dihedral_angle_d11.0752633
X-RAY DIFFRACTIONf_chiral_restr0.0461194
X-RAY DIFFRACTIONf_plane_restr0.0031324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5489-2.61260.32681320.27992383X-RAY DIFFRACTION87
2.6126-2.68320.27771530.26662548X-RAY DIFFRACTION94
2.6832-2.76220.33981490.25492677X-RAY DIFFRACTION98
2.7622-2.85130.29131420.25132706X-RAY DIFFRACTION99
2.8513-2.95320.28521400.24532738X-RAY DIFFRACTION99
2.9532-3.07130.32631380.24782700X-RAY DIFFRACTION99
3.0713-3.2110.28351280.23672761X-RAY DIFFRACTION99
3.211-3.38020.25981410.22482725X-RAY DIFFRACTION99
3.3802-3.59180.25231420.20482711X-RAY DIFFRACTION99
3.5918-3.86880.24031540.18832730X-RAY DIFFRACTION98
3.8688-4.25760.17371450.16322734X-RAY DIFFRACTION98
4.2576-4.87240.19051410.14492735X-RAY DIFFRACTION99
4.8724-6.13380.18761670.17352754X-RAY DIFFRACTION98
6.1338-35.95060.22211220.18292859X-RAY DIFFRACTION96
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)
10.58770.655-0.72823.5565-0.69921.05270.17630.07610.12310.1363-0.1826-1.1356-0.14490.1263-0.01180.3793-0.0077-0.03680.52410.09181.0828.537360.397133.7802
21.06680.4466-0.9513.67190.21861.34260.0285-0.10530.07460.7139-0.1949-0.4603-0.06490.08540.19410.5455-0.0009-0.23320.42910.02410.470112.516135.097754.9806
30.763-0.96251.56863.7769-1.30043.4029-0.477-0.5010.58720.2212-0.43631.3974-0.63050.34680.86230.95420.233-0.24011.0318-0.29171.00920.866656.345153.2452
41.56830.30150.30581.06440.6182.3234-0.0013-0.08820.02020.1673-0.0290.1523-0.0358-0.35240.04670.28820.0437-0.03910.37760.0460.31142.32537.554740.9
50.63710.09020.00722.3933-0.31730.7113-0.03680.07360.0671-0.054-0.0726-0.41680.0367-0.03930.08940.28510.01740.02230.38-0.01640.34377.341545.622429.6454
61.3734-0.13320.17452.4575-1.14311.92520.00930.29710.1081-0.83-0.127-0.45660.27910.13720.07950.56180.05380.20060.49070.04380.34238.01850.37919.947
71.4333-0.62690.0211.0820.80180.81020.02610.5915-0.6711-0.7516-0.3281-0.32611.45140.03520.2671.26330.12850.23190.5905-0.14820.74649.520921.642419.1902
81.82250.4659-0.10222.0775-0.17090.3875-0.05320.6488-0.0627-0.82720.0317-0.06530.2293-0.00250.04730.73660.01370.07580.55410.02580.3205-1.47848.2894.7094
92.1852-0.1687-0.32172.09050.15873.0978-0.1449-0.1776-0.24130.00090.01940.42130.2424-0.19220.12640.3256-0.01680.00780.37110.0530.4555-18.752137.720332.6687
102.06851.670.04161.34360.0345-0.0006-0.1342-1.4472-0.3106-0.2669-0.8024-0.4253-0.1106-0.04230.88180.6175-0.142-0.18930.8587-0.01260.7358-36.766332.429415.1113
112.2842-1.12212.04653.57931.15363.3845-0.52350.8624-0.2035-0.22660.73711.2180.9295-0.42350.10340.6940.0840.0051.18270.12211.4058-33.968458.236129.7864
127.7817-2.99221.61388.6112-1.2887.0085-0.67841.01771.67250.46990.8250.9336-0.9134-0.48660.03920.401-0.0075-0.05910.5720.08820.8253-16.914957.272733.8098
132.72630.52920.69463.9037-0.06510.1905-0.18130.4572-0.0165-0.86040.396-0.6995-0.1627-0.4319-0.34040.44890.00960.05760.53590.01130.3969-8.149947.35124.7876
145.5613-2.3674-1.75326.9106-2.51882.4338-0.2239-1.11730.82561.10330.1625-0.1908-0.24830.15070.06850.46990.03390.03840.5811-0.07490.46034.643158.472730.4364
154.73741.85780.73110.89510.53990.4914-0.7720.28841.4208-1.02560.25260.3462-0.0192-0.09840.5710.4449-0.0547-0.06040.54280.15560.7312-10.147755.212121.8924
164.8374-0.7925-2.69823.7555-0.37954.2421-0.1450.66720.82050.22180.28390.6665-0.277-1.47560.16910.39750.0640.05560.71340.04110.684-23.170251.576331.8097
171.8855-0.2610.67290.0788-0.01320.3642-1.03230.68630.70430.80420.419-0.01960.36610.93280.42580.61360.1924-0.04010.85260.01671.4363-37.431663.877732.5923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:108)
2X-RAY DIFFRACTION2(chain A and resid 109:250)
3X-RAY DIFFRACTION3(chain A and resid 251:261)
4X-RAY DIFFRACTION4(chain A and resid 262:310)
5X-RAY DIFFRACTION5(chain A and resid 311:413)
6X-RAY DIFFRACTION6(chain A and resid 414:510)
7X-RAY DIFFRACTION7(chain A and resid 511:557)
8X-RAY DIFFRACTION8(chain A and resid 558:683)
9X-RAY DIFFRACTION9(chain A and resid 684:883)
10X-RAY DIFFRACTION10(chain A and resid 884:902)
11X-RAY DIFFRACTION11(chain P and resid 102:107)
12X-RAY DIFFRACTION12(chain P and resid 108:111)
13X-RAY DIFFRACTION13(chain P and resid 112:115)
14X-RAY DIFFRACTION14(chain T and resid 1:4)
15X-RAY DIFFRACTION15(chain T and resid 5:8)
16X-RAY DIFFRACTION16(chain T and resid 9:12)
17X-RAY DIFFRACTION17(chain T and resid 13:18)

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