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Basic information

Entry
Database: PDB / ID: 2pyj
TitlePhi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)
Components
  • 5'-d(ACACGTAAGCAGTC)-3'
  • 5'-d(GACTGCTTA(DOC)-3'
  • DNA polymerase
KeywordsREPLICATION / TRANSFERASE/DNA / protein-dna complex / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


nucleoside binding / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / exonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
TPR 1 domain of DNA polymerase / TPR 1 domain of DNA polymerase / DNA polymerase; domain 5 / DNA-directed DNA polymerase, family B, mitochondria/virus / DNA-directed DNA polymerase, family B, phi29-like virus / DNA polymerase type B, organellar and viral / DNA polymerase; domain 6 / Rhinovirus 14, subunit 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase ...TPR 1 domain of DNA polymerase / TPR 1 domain of DNA polymerase / DNA polymerase; domain 5 / DNA-directed DNA polymerase, family B, mitochondria/virus / DNA-directed DNA polymerase, family B, phi29-like virus / DNA polymerase type B, organellar and viral / DNA polymerase; domain 6 / Rhinovirus 14, subunit 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Few Secondary Structures / Irregular / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBerman, A.J. / Kamtekar, S. / Goodman, J.L. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A.
CitationJournal: Embo J. / Year: 2007
Title: Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases
Authors: Berman, A.J. / Kamtekar, S. / Goodman, J.L. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 15, 2020Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
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_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_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_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 1.5Aug 30, 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
X: 5'-d(GACTGCTTA(DOC)-3'
Y: 5'-d(ACACGTAAGCAGTC)-3'
Q: 5'-d(GACTGCTTA(DOC)-3'
R: 5'-d(ACACGTAAGCAGTC)-3'
K: 5'-d(ACACGTAAGCAGTC)-3'
J: 5'-d(GACTGCTTA(DOC)-3'
A: DNA polymerase
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,99355
Polymers155,2758
Non-polymers3,71847
Water17,457969
1
X: 5'-d(GACTGCTTA(DOC)-3'
Y: 5'-d(ACACGTAAGCAGTC)-3'
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,88927
Polymers73,9993
Non-polymers1,89024
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: 5'-d(GACTGCTTA(DOC)-3'
R: 5'-d(ACACGTAAGCAGTC)-3'
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,64023
Polymers73,9993
Non-polymers1,64220
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: 5'-d(ACACGTAAGCAGTC)-3'
J: 5'-d(GACTGCTTA(DOC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4645
Polymers7,2782
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.835, 114.667, 104.761
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 6 molecules XQJYRK

#1: DNA chain 5'-d(GACTGCTTA(DOC)-3'


Mass: 3003.992 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain 5'-d(ACACGTAAGCAGTC)-3'


Mass: 4273.806 Da / Num. of mol.: 3 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein DNA polymerase / E.C.2.7.7.7 / Early protein GP2


Mass: 66720.914 Da / Num. of mol.: 2 / Mutation: D12A,D66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: 2, gp2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03680, DNA-directed DNA polymerase

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Non-polymers , 5 types, 1016 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 200 mM ammonium acetate, 15% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2ammonium acetate11
3PEG 400011
4sodium acetate12
5ammonium acetate12
6PEG 400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2006
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 109968 / Num. obs: 107450 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.3
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / % possible all: 83.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: copy c of 1xhx without residues 359-394

1xhx


Resolution: 2.03→41.07 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.068 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23409 5354 5 %RANDOM
Rwork0.18904 ---
obs0.19128 102064 97.68 %-
all-104147 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.585 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.03→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9367 1431 230 969 11997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211424
X-RAY DIFFRACTIONr_bond_other_d0.0030.027624
X-RAY DIFFRACTIONr_angle_refined_deg1.1712.13615620
X-RAY DIFFRACTIONr_angle_other_deg2.205318575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27251153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56624.028432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.753151768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5361540
X-RAY DIFFRACTIONr_chiral_restr0.070.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022184
X-RAY DIFFRACTIONr_nbd_refined0.1950.21940
X-RAY DIFFRACTIONr_nbd_other0.2150.27464
X-RAY DIFFRACTIONr_nbtor_refined0.1880.24966
X-RAY DIFFRACTIONr_nbtor_other0.0850.25164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2951
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.98247542
X-RAY DIFFRACTIONr_mcbond_other0.18442325
X-RAY DIFFRACTIONr_mcangle_it2.03469219
X-RAY DIFFRACTIONr_scbond_it1.90547488
X-RAY DIFFRACTIONr_scangle_it2.04866392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.034→2.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 295 -
Rwork0.24 6055 -
obs--78.3 %

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