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- PDB-3s9h: RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary comp... -

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Basic information

Entry
Database: PDB / ID: 3s9h
TitleRB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+
Components
  • 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-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: 1.95 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 1, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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
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*(DOC))-3'
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,71611
Polymers113,9683
Non-polymers7488
Water20,8071155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-85 kcal/mol
Surface area43120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.050, 119.821, 130.791
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*(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: 104490.945 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, 1163 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1155 / 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: 52.33 %
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: NSLS / Beamline: X29A / Wavelength: 1.21448 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21448 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. all: 86562 / Num. obs: 83597 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.73
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 0.934 / Num. unique all: 9629 / % possible all: 57.9

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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: 1.95→63.63 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.858 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21302 4205 5 %RANDOM
Rwork0.17057 ---
obs0.1727 79392 96.56 %-
all-82220 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0 Å2
2---0.45 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 629 35 1155 9181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0228326
X-RAY DIFFRACTIONr_angle_refined_deg0.8682.06111398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7385918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59624.195379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9081547
X-RAY DIFFRACTIONr_chiral_restr0.060.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216162
X-RAY DIFFRACTIONr_mcbond_it1.02744529
X-RAY DIFFRACTIONr_mcangle_it1.80267349
X-RAY DIFFRACTIONr_scbond_it2.11363797
X-RAY DIFFRACTIONr_scangle_it3.24794041
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 227 -
Rwork0.306 4081 -
obs--68.25 %
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)
10.42040.0714-0.13710.0598-0.00870.1139-0.1238-0.03480.1407-0.04640.07640.0670.0453-0.0420.04740.13260.021-0.03120.221-0.00690.1646-17.08557.17529.843
20.22970.1397-0.10671.4755-0.39190.31640.0036-0.02960.05110.0654-0.0406-0.0898-0.03680.06620.0370.1218-0.0095-0.00810.15920.0040.055325.10562.39731.657
30.32010.2721-0.00580.93850.01491.34220.021-0.04080.01250.1312-0.05360.00930.0608-0.09470.03270.1214-0.0043-0.00660.1506-0.00460.015310.53937.93750.473
40.73890.4751-0.17960.9106-0.06170.3415-0.05620.22340.0276-0.17360.10450.03460.0112-0.0815-0.04830.1558-0.0215-0.01990.19990.02060.0096-3.60553.2324.928
50.39840.29010.00822.90220.27330.1948-0.06230.0604-0.10280.0650.0432-0.05950.0620.03780.01910.15320.00650.00760.176-0.01130.03089.4933.6118.112
61.288-0.3048-0.51430.6373-0.09960.6091-0.04620.0443-0.0965-0.05570.07360.01970.03430.0289-0.02750.1476-0.03-0.00190.17480.00390.0343-9.35237.05317.141
71.6301-0.09920.24540.68350.25751.3252-0.1041-0.3049-0.10290.07820.11590.12890.0201-0.1256-0.01180.07120.02770.02640.17020.06470.0376-22.28939.3737.552
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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