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- PDB-1s5j: Insight in DNA Replication: The crystal structure of DNA Polymera... -

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Basic information

Entry
Database: PDB / ID: 1s5j
TitleInsight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus
ComponentsDNA polymerase I
KeywordsTRANSFERASE / DNA POLYMERASE / REPLICATION / DISULFIDE BONDS
Function / homology
Function and homology information


exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
Helix Hairpins - #1390 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / 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 ...Helix Hairpins - #1390 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / 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 / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSavino, C. / Federici, L. / Nastopoulos, V. / Johnson, K.A. / Pisani, F.M. / Rossi, M. / Tsernoglou, D.
Citation
Journal: Structure / Year: 2004
Title: Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus
Authors: Savino, C. / Federici, L. / Johnson, K.A. / Vallone, B. / Nastopoulos, V. / Rossi, M. / Pisani, F.M. / Tsernoglou, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies of DNA polymerase from the thermophilic archaeon Sulfolobus solfataricus
Authors: Nastopoulos, V. / Pisani, F.M. / Savino, C. / Federici, L. / Rossi, M. / Tsernoglou, D.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,41811
Polymers97,5291
Non-polymers88910
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.470, 68.800, 125.850
Angle α, β, γ (deg.)90.00, 107.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA polymerase I /


Mass: 97528.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: MT 4 / Gene: DPO1, POLS, SSO0552 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26811, DNA-directed DNA polymerase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2000
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 59688 / Num. obs: 59688 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 4.1
Reflection shellResolution: 2.4→2.46 Å / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.117 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27222 3011 5 %RANDOM
Rwork0.23246 ---
all0.264 56677 --
obs0.23443 56677 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.581 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å2-2.09 Å2
2---1.99 Å20 Å2
3---3.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 46 248 6230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226103
X-RAY DIFFRACTIONr_bond_other_d0.0020.025599
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9758256
X-RAY DIFFRACTIONr_angle_other_deg0.825313061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026566
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021223
X-RAY DIFFRACTIONr_nbd_refined0.1950.21306
X-RAY DIFFRACTIONr_nbd_other0.2130.26585
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6961.53625
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29925903
X-RAY DIFFRACTIONr_scbond_it1.56832478
X-RAY DIFFRACTIONr_scangle_it2.6444.52353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 204
Rwork0.284 4038

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