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- PDB-6joq: Crystal structures of phage NrS-1 N300-dNTPs-Mg2+ complex provide... -

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Basic information

Entry
Database: PDB / ID: 6joq
TitleCrystal structures of phage NrS-1 N300-dNTPs-Mg2+ complex provide molecular mechanisms for substrate specificity
ComponentsPrimase
KeywordsREPLICATION / Prim-pol / Primase
Function / homology
Function and homology information


viral DNA genome replication / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA helicase / DNA replication / DNA-directed DNA polymerase / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA Primase-polymerase
Similarity search - Component
Biological speciesNitratiruptor phage NrS-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuo, H.J. / Li, M.J. / Wu, H. / 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 structures of phage NrS-1 N300-dNTPs-Mg2+complex provide molecular mechanisms for substrate specificity.
Authors: Guo, H. / Li, M. / Wu, H. / Wang, W. / Yu, F. / He, J.
History
DepositionMar 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8714
Polymers36,3151
Non-polymers5563
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.360, 55.388, 50.774
Angle α, β, γ (deg.)90.000, 95.480, 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: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14433 / % possible obs: 98.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Χ2: 0.959 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.51.2716530.5410.6181.420.9888.4
2.44-2.494.71.2686460.5610.611.4140.93590.7
2.49-2.535.41.1937060.6610.5461.3180.9895.4
2.53-2.596.30.9537150.8310.4051.0380.98799.4
2.59-2.646.50.9337420.8320.3921.0140.997100
2.64-2.76.70.8737220.8750.3610.9461.058100
2.7-2.776.90.6727380.9170.2730.7261.01399.7
2.77-2.856.90.5917100.9190.240.6390.97399.2
2.85-2.9370.457360.9560.1820.4861.02299.7
2.93-3.026.80.3137280.9740.1290.3391.02699.5
3.02-3.136.70.2547320.9790.1060.2761.01299.3
3.13-3.266.10.1617090.9850.070.1761.02197
3.26-3.416.90.137420.9920.0530.141.05199.9
3.41-3.587.10.17200.9960.040.1081.045100
3.58-3.8170.0737290.9970.030.0790.98999.9
3.81-4.16.90.0547370.9980.0220.0580.87999.6
4.1-4.526.80.0447310.9980.0180.0480.80998
4.52-5.176.30.0417290.9980.0170.0440.79398.1
5.17-6.5170.0417480.9980.0160.0440.71299.9
6.51-506.40.0427600.9980.0180.0460.91897.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A9W

6a9w


Resolution: 2.4→38.588 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2321 546 4.72 %
Rwork0.1931 --
obs0.1949 11577 78.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.22 Å2 / Biso mean: 42.8304 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 2.4→38.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 33 73 2360
Biso mean--40.82 37.36 -
Num. residues----280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-2.64160.3284670.26431258132536
2.6416-3.02380.33571200.25532808292880
3.0238-3.80910.25111710.20013452362399
3.8091-38.59330.1861880.16343513370199
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)
10.0282-0.0018-0.01340.0953-0.0440.04380.0604-0.01210.03980.17010.0858-0.1405-0.00680.09650.10980.0673-0.012-0.0740.0498-0.19180.0955-21.2043-10.009428.0093
20.00680.0021-0.00020.0117-0.00050.017-0.00040.026-0.0539-0.02170.05-0.04470.020.01610.03430.24650.03370.01440.2476-0.24770.1966-22.102117.7745.8923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 170 )A1 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 294 )A171 - 294

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