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

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Basic information

Entry
Database: PDB / ID: 3sjj
TitleRB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+
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 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
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: 2.38 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 21, 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_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.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_conn.ptnr2_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
A: DNA polymerase
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,79211
Polymers113,9403
Non-polymers8528
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-51 kcal/mol
Surface area43610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.560, 118.217, 130.108
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 , 1 types, 1 molecules A

#1: 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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DNA chain , 2 types, 2 molecules TP

#2: 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
#3: 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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Non-polymers , 3 types, 146 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
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: Nov 1, 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: 2.35→50 Å / Num. all: 51283 / Num. obs: 45847 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 10
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1 / Num. unique all: 3930 / % possible all: 77.9

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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: 2.38→47.25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 20.701 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.459 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26543 2286 5.1 %RANDOM
Rwork0.20164 ---
obs0.20482 42465 91.25 %-
all-46537 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.893 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0 Å2
2--0.63 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.38→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 630 35 138 8146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228264
X-RAY DIFFRACTIONr_angle_refined_deg1.1212.06211306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5424.182373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.308151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661546
X-RAY DIFFRACTIONr_chiral_restr0.0730.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216098
X-RAY DIFFRACTIONr_mcbond_it1.73244498
X-RAY DIFFRACTIONr_mcangle_it3.01267290
X-RAY DIFFRACTIONr_scbond_it3.32763766
X-RAY DIFFRACTIONr_scangle_it4.90994015
LS refinement shellResolution: 2.384→2.446 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 119 -
Rwork0.28 2072 -
obs--61.37 %
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)
13.4466-0.6715-0.32291.018-0.07770.1536-0.1677-0.18230.2407-0.09540.09230.20440.0056-0.02460.07550.16770.0623-0.02180.1457-0.04690.2671-17.16555.08329.022
20.36480.4045-0.39832.836-0.61840.71560.04970.00920.02010.0321-0.014-0.2988-0.06670.077-0.03570.152-0.0051-0.00650.0286-0.02110.243325.19559.4332.756
30.88430.05670.05521.4932-0.01661.71650.0271-0.08360.03750.2178-0.07850.06360.1364-0.10110.05140.2471-0.0021-0.03080.0369-0.03130.08438.96735.4851.418
41.11440.323-0.05971.60980.27880.44830.06310.37860.0491-0.2849-0.0157-0.051-0.0531-0.0912-0.04740.26110.03070.03330.15430.01940.0122-2.25949.854.572
50.32590.5186-0.0274.69510.45480.6512-0.01440.1364-0.10080.0018-0.0432-0.14760.16910.0340.05760.25690.03010.02330.089-0.05320.13569.72730.43718.965
60.5571-0.00110.1940.8094-0.90981.20720.01520.1759-0.08810.00640.08620.05790.1301-0.1265-0.10140.1985-0.0664-0.0070.1258-0.050.1348-9.23134.40917.208
72.6135-0.39580.64390.89260.34472.2333-0.2409-0.4553-0.31460.13370.22790.144-0.0651-0.39420.0130.13580.07230.06630.17920.0630.0947-22.85338.04536.997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A902
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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