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- PDB-2atq: RB69 single-stranded DNA binding protein-DNA polymerase fusion -

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Basic information

Entry
Database: PDB / ID: 2atq
TitleRB69 single-stranded DNA binding protein-DNA polymerase fusion
Components
  • DNA polymerase
  • gp32
KeywordsTRANSFERASE/DNA BINDING PROTEIN / DNA polymerase / palm domain / fingers domain / thumb domain / single-stranded DNA binding protein / OB-fold / TRANSFERASE-DNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / single-stranded DNA binding / DNA recombination ...bidirectional double-stranded viral DNA replication / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / single-stranded DNA binding / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Replication Fork Single-Stranded DNA Binding Protein / Replication Fork Single-Stranded Dna Binding Protein / Bacteriophage T4, Gp32, single-stranded DNA-binding domain / Bacteriophage T4, Gp32, single-stranded DNA-binding superfamily / Bacteriophage T4, Gp32, single-stranded DNA-binding / gp32 DNA binding protein like / Monooxygenase - #300 / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 ...Replication Fork Single-Stranded DNA Binding Protein / Replication Fork Single-Stranded Dna Binding Protein / Bacteriophage T4, Gp32, single-stranded DNA-binding domain / Bacteriophage T4, Gp32, single-stranded DNA-binding superfamily / Bacteriophage T4, Gp32, single-stranded DNA-binding / gp32 DNA binding protein like / Monooxygenase - #300 / 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 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-directed DNA polymerase, family B, multifunctional 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 / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / DNA-directed DNA polymerase / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsSun, S. / Geng, L. / Shamoo, Y.
CitationJournal: Proteins / Year: 2006
Title: Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity.
Authors: Sun, S. / Geng, L. / Shamoo, Y.
History
DepositionAug 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE C-TERMINUS OF RB69 SINGLE-STRANDED DNA BINDING PROTEIN CORE DOMAIN IS FUSED TO THE N- ...SEQUENCE THE C-TERMINUS OF RB69 SINGLE-STRANDED DNA BINDING PROTEIN CORE DOMAIN IS FUSED TO THE N-TERMINUS OF DNA POLYMERASE THROUGH A LINKER CONSISTING OF GTGSGT. THE LINKER WAS NOT OBSERVED IN THE DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
B: gp32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3924
Polymers130,8842
Non-polymers5092
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.029, 196.029, 85.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA polymerase / / Gp43


Mass: 104655.141 Da / Num. of mol.: 1 / Mutation: D222A, D327A
Source method: isolated from a genetically manipulated source
Details: C-terminus is fused to a linker not seen in the density
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: 43 / Plasmid: pET101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: Protein gp32


Mass: 26228.523 Da / Num. of mol.: 1 / Fragment: RB69 single-stranded DNA binding protein
Source method: isolated from a genetically manipulated source
Details: N-terminus is fused to a linker not seen in the density
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: gp32 / Plasmid: pET101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7Y265
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 3.6 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, Tris-Cl, 6-aminocaproic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
Reflection

D res high: 3.2 Å / D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2% possible obs
5.11599060.099199.8
4.92596150.1120.93399.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.895098.910.0291.2035.1
5.476.8999.910.0711.2335.1
4.785.4799.910.0771.315.1
4.344.7810010.0790.9755.1
4.034.3410010.10.8715.2
3.794.0310010.1530.945.1
3.63.7910010.2320.9455.1
3.453.610010.3140.8595.1
3.313.4510010.4530.8735.1
3.23.3199.610.5890.7744.6
6.89509920.0260.8695.1
5.476.8999.920.0781.0435.1
4.785.4799.920.0881.1725.1
4.344.7810020.0960.9255.1
4.034.3410020.1310.8655.2
3.794.0310020.2130.9445.1
3.63.7910020.3330.9655.1
3.453.610020.460.8425.1
3.313.4599.920.6410.8624.6
3.23.3194.520.7810.7583.5
ReflectionResolution: 3.1→50 Å / Num. all: 34157 / Num. obs: 33922 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 85.8 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Χ2: 1.164 / Net I/σ(I): 19.5
Reflection shellResolution: 3.1→3.21 Å / % possible obs: 94.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 3205 / Num. unique all: 3205 / Rsym value: 0.646 / Χ2: 0.823 / % possible all: 94.9

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.362 / Packing: 0.328
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.9 0
Translation4 Å15 Åphased99.9 0
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 30807

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
DM5phasing
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: PDB entry 1IH7, 2A1K

1ih7

2a1k


Resolution: 3.2→37.99 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.345 1492 5.1 %RANDOM
Rwork0.284 ---
all0.321 31027 --
obs0.321 29505 95.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 10 Å2 / ksol: 0.220869 e/Å3
Displacement parametersBiso max: 117.78 Å2 / Biso mean: 69.84 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-14.01 Å218.02 Å20 Å2
2--14.01 Å20 Å2
3----28.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Luzzati d res high-3.2
Refinement stepCycle: LAST / Resolution: 3.2→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8607 0 29 0 8636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_torsion_deg22.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.2-3.350.3931785.30.35731970.0293847337587.7
3.35-3.520.351895.30.31633750.0253849356492.6
3.52-3.740.3441825.10.27234130.0263865359593
3.74-4.030.2981724.70.24434830.0233859365594.7
4.03-4.440.2882025.40.23635190.023865372196.3
4.44-5.080.3261784.70.24536110.0243890378997.4
5.08-6.390.3841764.60.31136740.0293887385099
6.39-37.990.3732155.40.3137410.0253986395699.2

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