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- PDB-1xi1: Phi29 DNA polymerase ssDNA complex, monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 1xi1
TitlePhi29 DNA polymerase ssDNA complex, monoclinic crystal form
Components
  • 5'-D(P*TP*TP*TP*TP*T)-3'
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA polymerase / protein-primed / strand displacement / processivity / replication / 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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / 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 polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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 polymerase
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsKamtekar, S. / Berman, A.J. / Wang, J. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Correction of X-ray intensities from single crystals containing lattice-translocation defects
Authors: Wang, J. / Kamtekar, S. / Berman, A.J. / Steitz, T.A.
#1: Journal: To be Published
Title: Correction of X-ray intensities from single crystals containing lattice translocation defects
Authors: Wang, J. / Kamtekar, S. / Berman, A.J. / Steitz, T.A.
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 22, 2020Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(P*TP*TP*TP*TP*T)-3'
D: 5'-D(P*TP*TP*TP*TP*T)-3'
A: DNA polymerase
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4426
Polymers136,3944
Non-polymers492
Water4,234235
1
C: 5'-D(P*TP*TP*TP*TP*T)-3'
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2213
Polymers68,1972
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-21 kcal/mol
Surface area28400 Å2
MethodPISA
2
D: 5'-D(P*TP*TP*TP*TP*T)-3'
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2213
Polymers68,1972
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-20 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.557, 170.563, 68.813
Angle α, β, γ (deg.)90.00, 106.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(P*TP*TP*TP*TP*T)-3'


Mass: 1476.007 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA polymerase / / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P03680, DNA-directed DNA polymerase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Magnesium acetate, Tris-HCl, salt, ammonium sulfate, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium acetate11
2Tris-HClTris11
3salt11
4ammonium sulfate11
5PEG 800011
6Magnesium acetate12
7Tris-HClTris12
8salt12
9ammonium sulfate12
10PEG 800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 66719 / Num. obs: 66719 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.34 Å / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→19.71 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1729277.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 6490 9.7 %RANDOM
Rwork0.243 ---
all0.243 66719 --
obs0.243 66719 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7282 Å2 / ksol: 0.354766 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1-20.92 Å20 Å212.3 Å2
2---12.07 Å20 Å2
3----8.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9336 120 2 235 9693
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.91.5
X-RAY DIFFRACTIONc_mcangle_it4.312
X-RAY DIFFRACTIONc_scbond_it42
X-RAY DIFFRACTIONc_scangle_it5.572.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 1062 10.1 %
Rwork0.423 9495 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA_REP.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM

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