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- PDB-7rr4: Structure of Deep-Sea Phage NrS-1 Primase-Polymerase N300 in comp... -

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Basic information

Entry
Database: PDB / ID: 7rr4
TitleStructure of Deep-Sea Phage NrS-1 Primase-Polymerase N300 in complex with magnesium and pyrophosphate
ComponentsPrimase
KeywordsREPLICATION / primpol / denovo / polymerase / nrspol
Function / homology
Function and homology information


viral DNA genome replication / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA helicase / DNA-directed DNA polymerase / DNA replication / hydrolase activity / ATP binding
Similarity search - Function
: / : / NrS-1 polymerase-like head domain / NrS-1 polymerase-like, tail domain / : / NrS-1 polymerase HBD domain / Domain of unknown function DUF5906 / Family of unknown function (DUF5906) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PYROPHOSPHATE / DNA Primase-polymerase
Similarity search - Component
Biological speciesNitratiruptor phage NrS-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsWang, L. / Yu, C. / Sliz, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Frontiers in Microbiology / Year: 2021
Title: Molecular Dissection of the Primase and Polymerase Activities of Deep-Sea Phage NrS-1 Primase-Polymerase
Authors: Huang, F. / Lu, X. / Yu, C. / Sliz, P. / Wang, L. / Zhu, B.
History
DepositionAug 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7764
Polymers32,5501
Non-polymers2273
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.340, 56.903, 48.564
Angle α, β, γ (deg.)90.000, 93.602, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Primase


Mass: 32549.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratiruptor phage NrS-1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: M5AAG8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 800 mM sodium phosphate monobasic, 1200 mM potassium phosphate dibasic, and 100 mM sodium acetate (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→51.34 Å / Num. obs: 26979 / % possible obs: 98.29 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.66 Å2 / Rmerge(I) obs: 0.09634 / Net I/σ(I): 12.8
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 1.175 / Num. unique obs: 2708

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RR3

7rr3


Resolution: 1.86→51.34 Å / SU ML: 0.2667 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 1354 5.02 %
Rwork0.2159 25597 -
obs0.2167 26951 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.09 Å2
Refinement stepCycle: LAST / Resolution: 1.86→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 11 100 2225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352175
X-RAY DIFFRACTIONf_angle_d0.78142954
X-RAY DIFFRACTIONf_chiral_restr0.0471318
X-RAY DIFFRACTIONf_plane_restr0.007381
X-RAY DIFFRACTIONf_dihedral_angle_d8.2237297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.930.41161210.39482559X-RAY DIFFRACTION98.28
1.93-20.34771420.33532556X-RAY DIFFRACTION98.11
2-2.090.31541390.28952508X-RAY DIFFRACTION98.15
2.09-2.210.31541430.26292598X-RAY DIFFRACTION99.17
2.21-2.340.28871250.25092556X-RAY DIFFRACTION99.11
2.34-2.520.25271240.23842549X-RAY DIFFRACTION98.06
2.52-2.780.31061470.23752558X-RAY DIFFRACTION99.08
2.78-3.180.24981320.23812587X-RAY DIFFRACTION98.44
3.18-4.010.21741330.19182574X-RAY DIFFRACTION97.8
4.01-51.340.17551480.17682552X-RAY DIFFRACTION95.85

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