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- PDB-1ig9: Structure of the Replicating Complex of a Pol Alpha Family DNA Po... -

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Basic information

Entry
Database: PDB / ID: 1ig9
TitleStructure of the Replicating Complex of a Pol Alpha Family DNA Polymerase
Components
  • 5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'
  • 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*(DOC))-3'
  • DNA POLYMERASE
KeywordsTRANSFERASE/DNA / DNA polymerase / catalytic complex / fidelity / two metal ion mechanism / 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-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFranklin, M.C. / Wang, J. / Steitz, T.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase
Authors: Franklin, M.C. / Wang, J. / Steitz, T.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal Structure of a Pol Alpha Family Replication DNA Polymerase from Bacteriophage RB69
Authors: Wang, J. / Sattar, A.K. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Building a Replisome from Interacting Pieces: Sliding Clamp Complexed to a Peptide from DNA Polymerase and a Polymerase Editing Complex
Authors: Shamoo, Y. / Steitz, T.A.
History
DepositionApr 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: 5'-D(*AP*CP*AP*GP*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*CP*(DOC))-3'
A: DNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0898
Polymers114,4473
Non-polymers6425
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.787, 118.602, 127.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach monomer constitutes a functional assembly.

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Components

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DNA chain , 2 types, 2 molecules TP

#1: DNA chain 5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'


Mass: 5550.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Substrate DNA, template strand
#2: DNA chain 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*(DOC))-3'


Mass: 4240.768 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Substrate DNA, primer strand (dideoxy-terminated)

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Protein , 1 types, 1 molecules A

#3: Protein DNA POLYMERASE


Mass: 104655.141 Da / Num. of mol.: 1 / Mutation: Exonuclease-deficient (D222A/D327A) mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: gp43 / Plasmid: pRB.43 exo- / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase

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Non-polymers , 3 types, 361 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG 350 monomethyl ether, calcium chloride, sodium cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 350 monomethyl ether11
2calcium chloride11
3sodium cacodylate11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop / Details: Wang, J., (1997) Cell (Cambridge,Mass.), 89, 1087.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
20.05 Msodium citrate1drop
30.025 Msodium potassium tartrate1drop
40.5 Mammonium sulfate1drop
50.1 Msodium citrate1reservoir
60.5 Msodium potassium tartrate1reservoir
71.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 1999 / Details: double crystal monochromator
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: 2.6→30 Å / Num. all: 38733 / Num. obs: 38733 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.61

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CLQ, with non-protein atoms removed

1clq


Resolution: 2.6→29.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 297902.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh and Huber, as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3622 9.7 %RANDOM
Rwork0.197 ---
all0.197 38733 --
obs0.197 37266 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.16 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 61.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å20 Å20 Å2
2---2.7 Å20 Å2
3---7.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7355 650 33 356 8394
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it2.142
X-RAY DIFFRACTIONc_mcangle_it3.523
X-RAY DIFFRACTIONc_scbond_it5.044
X-RAY DIFFRACTIONc_scangle_it7.035
LS refinement shellResolution: 2.6→2.64 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 170 9.8 %
Rwork0.325 1564 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4TTP.PARTTP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.7 % / Rfactor all: 10
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it4
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it5
LS refinement shell
*PLUS
Rfactor Rfree: 0.396 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.325

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