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- PDB-4khw: Ternary complex of RB69 mutant L415F with ribonucleotide at -2 po... -

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Basic information

Entry
Database: PDB / ID: 4khw
TitleTernary complex of RB69 mutant L415F with ribonucleotide at -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*AP*G)-R(P*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-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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.371 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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_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.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_asym_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*AP*G)-R(P*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)115,36114
Polymers114,5133
Non-polymers84911
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-112 kcal/mol
Surface area41330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.355, 118.630, 126.310
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*AP*G)-R(P*G)-D(P*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5566.605 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 , 4 types, 545 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.: 8 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 MM TRIS-HCL, 19% PEG350, 180 MM CALCIUM CHLORIDE,, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.371→50 Å / Num. all: 46949 / Num. obs: 44309 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.37→2.44 Å / Rmerge(I) obs: 0.453 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE: 1.7_650)model building
PHENIX(PHENIX.REFINE: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.371→44.642 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2241 2413 4.98 %
Rwork0.1717 --
obs0.1743 44309 97.55 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8106 Å2-0 Å20 Å2
2---4.8129 Å20 Å2
3---4.0023 Å2
Refinement stepCycle: LAST / Resolution: 2.371→44.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 651 39 534 8434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078266
X-RAY DIFFRACTIONf_angle_d0.76411381
X-RAY DIFFRACTIONf_dihedral_angle_d11.4512763
X-RAY DIFFRACTIONf_chiral_restr0.0521206
X-RAY DIFFRACTIONf_plane_restr0.0031353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3713-2.41970.34831070.28272108X-RAY DIFFRACTION76
2.4197-2.47230.2771390.26512665X-RAY DIFFRACTION98
2.4723-2.52980.33061240.25882680X-RAY DIFFRACTION98
2.5298-2.5930.28261580.24642669X-RAY DIFFRACTION98
2.593-2.66310.2731590.23712691X-RAY DIFFRACTION99
2.6631-2.74150.30981490.242692X-RAY DIFFRACTION99
2.7415-2.830.26341460.22482713X-RAY DIFFRACTION99
2.83-2.93110.24781350.21652740X-RAY DIFFRACTION99
2.9311-3.04840.29491430.20992713X-RAY DIFFRACTION99
3.0484-3.18710.27321170.1952767X-RAY DIFFRACTION99
3.1871-3.35510.21071520.17792710X-RAY DIFFRACTION99
3.3551-3.56520.24171420.15762736X-RAY DIFFRACTION99
3.5652-3.84040.21321580.15052783X-RAY DIFFRACTION99
3.8404-4.22660.17091470.1292765X-RAY DIFFRACTION100
4.2266-4.83750.16891400.11572801X-RAY DIFFRACTION100
4.8375-6.09230.18771660.13272813X-RAY DIFFRACTION100
6.0923-44.64970.19391310.15392988X-RAY DIFFRACTION99
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)
10.40450.4896-0.27762.8687-0.91321.1440.08130.01270.03920.2432-0.1712-0.5838-0.14680.13670.09160.2333-0.01420.00070.31250.0740.586128.597963.051533.4564
21.13710.1801-0.27672.2585-0.59891.54060.0086-0.0453-0.04840.3668-0.1886-0.2630.1525-0.06980.09990.2716-0.0154-0.07250.25940.02350.254712.406130.724251.951
30.86740.8977-0.32581.65930.23632.44670.2189-0.18530.11320.3942-0.2432-0.3391-0.2504-0.02170.05420.2662-0.0411-0.10420.27270.01380.280815.566946.094852.9094
41.2902-0.39130.47790.6840.70751.68910.0634-0.0134-0.01050.15040.06140.15570.0932-0.5084-0.03780.25190.0096-0.00240.30150.03180.2499-0.162735.012739.1048
50.25370.06620.02181.1011-0.10750.67460.01240.01310.0701-0.1885-0.086-0.16780.1167-0.0280.03020.17860.01010.01090.22650.02120.21367.449146.02228.6433
61.0204-0.02390.25111.7191-0.23030.8638-0.00350.2465-0.0218-0.3466-0.0346-0.24940.36810.16840.03050.42470.09840.12610.2910.02220.18758.893242.444411.2923
71.06740.1296-0.05591.7015-0.21470.6694-0.0580.32960.0464-0.6420.04090.02370.3364-0.0141-0.01070.51680.01370.0210.34530.03430.1717-0.62246.45196.694
81.048-0.5388-0.31331.1530.20110.87640.00230.3305-0.2109-0.466-0.1020.1350.4026-0.06440.10780.6321-0.0139-0.02730.31-0.02320.2619-10.159834.255910.6847
91.6289-0.05460.03991.86610.14892.0637-0.0259-0.3091-0.07670.07430.04810.27480.0551-0.151-0.03960.1775-0.00820.0090.24750.04710.252-19.969838.333538.7335
101.11960.5335-0.29920.8768-0.1010.2762-0.1481-0.0311-0.0676-0.3975-0.19070.1354-0.1064-0.17320.29090.3697-0.0476-0.1020.43010.02150.4173-32.514134.535319.8224
113.3120.57860.20312.47720.48880.7554-0.55170.2949-0.3328-0.33070.12070.50950.9068-0.29370.12550.44180.03050.11080.75380.20641.214-35.662157.573529.831
125.2196-2.06212.36342.6128-0.84122.6915-0.40520.81561.0550.36420.29840.034-0.5984-0.03990.07720.2883-0.0196-0.02810.42390.12010.7385-19.858259.838731.9958
130.84880.2356-0.62350.3566-0.3870.8709-0.02280.35980.0845-0.01410.054-0.0967-0.0177-0.4137-0.04980.28030.00850.00710.35050.02210.3009-9.217448.284726.4601
142.1031-0.6721-0.72212.3049-0.8210.8406-0.1493-0.4520.3636-0.00880.09050.0621-0.0464-0.121-0.01590.19210.04840.02270.2910.00850.2398-2.980256.770325.7539
151.265-0.8925-1.60180.76120.99282.1394-0.10070.10430.16470.31950.07830.49450.3622-0.5023-0.03970.2880.02030.07850.5189-0.00580.5202-23.044351.290531.5379
162.38750.08780.9269-0.0040.05190.3291-0.95110.37350.80540.21780.2215-0.09580.08790.48170.13270.34010.18130.00030.50470.09510.9354-37.210863.89932.3277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:98)
2X-RAY DIFFRACTION2(chain A and resid 99:197)
3X-RAY DIFFRACTION3(chain A and resid 198:270)
4X-RAY DIFFRACTION4(chain A and resid 271:310)
5X-RAY DIFFRACTION5(chain A and resid 311:416)
6X-RAY DIFFRACTION6(chain A and resid 417:541)
7X-RAY DIFFRACTION7(chain A and resid 542:683)
8X-RAY DIFFRACTION8(chain A and resid 684:724)
9X-RAY DIFFRACTION9(chain A and resid 725:870)
10X-RAY DIFFRACTION10(chain A and resid 871:902)
11X-RAY DIFFRACTION11(chain P and resid 102:106)
12X-RAY DIFFRACTION12(chain P and resid 107:110)
13X-RAY DIFFRACTION13(chain P and resid 111:115)
14X-RAY DIFFRACTION14(chain T and resid 1:8)
15X-RAY DIFFRACTION15(chain T and resid 9:12)
16X-RAY DIFFRACTION16(chain T and resid 13:18)

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