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- PDB-2pzs: Phi29 DNA polymerase complexed with primer-template DNA (post-tra... -

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Basic information

Entry
Database: PDB / ID: 2pzs
TitlePhi29 DNA polymerase complexed with primer-template DNA (post-translocation binary complex)
Components
  • 5'-d(CTAACACGTAAGCAGTC)-3'
  • 5'-d(GACTGCTTAC)-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
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 18, 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 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 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(GACTGCTTAC)-3'
Y: 5'-d(CTAACACGTAAGCAGTC)-3'
T: 5'-d(CTAACACGTAAGCAGTC)-3'
U: 5'-d(CTAACACGTAAGCAGTC)-3'
R: 5'-d(GACTGCTTAC)-3'
S: 5'-d(CTAACACGTAAGCAGTC)-3'
A: DNA polymerase
B: DNA polymerase
C: DNA polymerase
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)293,64510
Polymers293,64510
Non-polymers00
Water1,60389
1
X: 5'-d(GACTGCTTAC)-3'
Y: 5'-d(CTAACACGTAAGCAGTC)-3'
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)74,9213
Polymers74,9213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
T: 5'-d(CTAACACGTAAGCAGTC)-3'
B: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)71,9012
Polymers71,9012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
U: 5'-d(CTAACACGTAAGCAGTC)-3'
C: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)71,9012
Polymers71,9012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
R: 5'-d(GACTGCTTAC)-3'
S: 5'-d(CTAACACGTAAGCAGTC)-3'
D: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)74,9213
Polymers74,9213
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.633, 146.292, 115.054
Angle α, β, γ (deg.)90.00, 117.93, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly contains one molecule of polymerase bound to primer-template DNA. Each asymmetric unit contains two complete biological assemblies and two complexes in which most of the DNA is disordered.

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Components

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


Mass: 3019.991 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain
5'-d(CTAACACGTAAGCAGTC)-3'


Mass: 5180.388 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
DNA polymerase / E.C.2.7.7.7 / Early protein GP2


Mass: 66720.914 Da / Num. of mol.: 4 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, 20% PEG 10000, 200 mM magnesium chloride, pH 8.5, 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: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2005
RadiationMonochromator: double flat Si crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 97325 / Num. obs: 95762 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 5.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: copy c of 1XHX without residues 358-394

1xhx


Resolution: 2.6→45.22 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.859 / SU B: 25.272 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.012 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27524 9703 10.1 %RANDOM
Rwork0.21872 ---
obs0.22452 85919 98.32 %-
all-97325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.26 Å2
2--0.01 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18487 1207 0 89 19783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02220310
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213781
X-RAY DIFFRACTIONr_angle_refined_deg1.2392.0427657
X-RAY DIFFRACTIONr_angle_other_deg0.87333645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77852256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87524.135844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.311153473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0261574
X-RAY DIFFRACTIONr_chiral_restr0.0830.22964
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024065
X-RAY DIFFRACTIONr_nbd_refined0.2070.24039
X-RAY DIFFRACTIONr_nbd_other0.1850.213280
X-RAY DIFFRACTIONr_nbtor_refined0.1930.29459
X-RAY DIFFRACTIONr_nbtor_other0.0830.210539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1881.514756
X-RAY DIFFRACTIONr_mcbond_other0.2211.54610
X-RAY DIFFRACTIONr_mcangle_it1.491218208
X-RAY DIFFRACTIONr_scbond_it1.344211554
X-RAY DIFFRACTIONr_scangle_it1.8942.59449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 716 -
Rwork0.362 5998 -
obs--93.57 %

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