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- PDB-6a9w: Structure of the bifunctional DNA primase-polymerase from phage NrS-1 -

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Basic information

Entry
Database: PDB / ID: 6a9w
TitleStructure of the bifunctional DNA primase-polymerase from phage NrS-1
ComponentsPrimase
KeywordsREPLICATION / prim-pol
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
DNA Primase-polymerase
Similarity search - Component
Biological speciesNitratiruptor phage NrS-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGuo, H.J. / Li, M.J. / Wang, T.L. / Wu, H. / Zhou, H. / Xu, C.Y. / Liu, X.P. / Yu, F. / He, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570740 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure and biochemical studies of the bifunctional DNA primase-polymerase from phage NrS-1.
Authors: Guo, H.J. / Li, M.J. / Wang, T.L. / Wu, H. / Zhou, H. / Xu, C.Y. / Liu, X.P. / Yu, F. / He, J.H.
History
DepositionJul 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Primase


Theoretical massNumber of molelcules
Total (without water)36,3151
Polymers36,3151
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15560 Å2
Unit cell
Length a, b, c (Å)119.874, 57.570, 47.631
Angle α, β, γ (deg.)90.000, 94.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Primase


Mass: 36314.852 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM Bis-Tris, pH 6.5, 0.2M Li2SO4, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→38.54 Å / Num. obs: 30021 / % possible obs: 99.7 % / Redundancy: 36.8 % / Biso Wilson estimate: 26.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.013 / Rrim(I) all: 0.078 / Net I/σ(I): 32.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8436.81.04217580.9710.1731.05799.5
9-38.5429.80.05121210.010.05280.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.54 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.37
RfactorNum. reflection% reflection
Rfree0.2184 1479 4.97 %
Rwork0.1784 --
obs0.1803 29779 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.33 Å2 / Biso mean: 38.0954 Å2 / Biso min: 16.75 Å2
Refinement stepCycle: final / Resolution: 1.8→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 0 158 2422
Biso mean---43.99 -
Num. residues----281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8002-1.85830.30251240.24872539266398
1.8583-1.92470.30761490.232537268699
1.9247-2.00180.22311190.20242551267098
2.0018-2.09290.2111480.18682532268099
2.0929-2.20320.27321310.1962578270999
2.2032-2.34120.23321500.18532560271099
2.3412-2.5220.22821310.19112572270399
2.522-2.77570.21251370.18992598273599
2.7757-3.17720.22731400.194425962736100
3.1772-4.00230.1931330.156426102743100
4.0023-38.5490.19771170.15882627274498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3602-1.1981-0.95623.87421.13361.5950.0289-0.13490.3460.11050.07590.0335-0.10780.0309-0.09070.1613-0.0121-0.00970.1902-0.04270.2242-13.6045-11.6224-22.1077
21.6815-0.11770.1310.9192-0.36550.16040.0146-0.1335-0.26150.181-0.03130.223-0.0468-0.1010.12120.1153-0.00110.01070.0609-0.12030.1911-20.37265.6896-38.3858
30.0059-0.0015-0.00230.00940.00550.00520.00120.0831-0.0682-0.015-0.07150.02860.0134-0.0274-0.01910.24550.0143-0.01820.2937-0.14010.2475-14.209719.5338-43.6145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 170 )A0 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 202 )A171 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 294 )A203 - 294

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