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

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Basic information

Entry
Database: PDB / ID: 6jon
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
Domain of unknown function DUF5906 / Family of unknown function (DUF5906) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA Primase-polymerase
Similarity search - Component
Biological speciesNitratiruptor phage NrS-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.2Oct 30, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3Nov 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)36,8554
Polymers36,3151
Non-polymers5403
Water18010
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 area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.820, 55.290, 50.550
Angle α, β, γ (deg.)90.000, 96.060, 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
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Nitratiruptor phage NrS-1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: M5AAG8
#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
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: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.34→36.584 Å / Num. obs: 29520 / % possible obs: 97.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.6
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.252 / Num. unique obs: 8011 / % possible all: 96.4

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A9W

6a9w


Resolution: 2.34→36.584 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.36 / Phase error: 32
RfactorNum. reflection% reflection
Rfree0.2334 1436 4.86 %
Rwork0.2233 --
obs0.2238 29520 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.99 Å2 / Biso mean: 76.4602 Å2 / Biso min: 40.95 Å2
Refinement stepCycle: final / Resolution: 2.34→36.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 32 10 2297
Biso mean--75 61.56 -
Num. residues----280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3401-2.42370.38411360.39922818295496
2.4237-2.52070.38021300.37882826295697
2.5207-2.63540.35281370.34362798293597
2.6354-2.77430.32941840.31252812299698
2.7743-2.9480.34421450.30552805295097
2.948-3.17560.30361340.2762746288093
3.1756-3.49490.2471290.23082833296297
3.4949-4.00010.22971630.19672850301398
4.0001-5.03760.15371390.16842853299297
5.0376-36.58810.19891390.18612743288294
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)
16.2392-0.3476-1.57793.27962.58317.0947-0.08610.00560.02580.38280.3053-0.46150.41010.6853-0.17680.60320.0656-0.1270.5005-0.0970.5936-14.523810.9596-3.269
24.6705-1.47750.81185.3782-0.27733.82310.1668-0.42560.37450.54630.0681-0.21650.04360.2331-0.16940.7999-0.0059-0.01080.5364-0.11770.5838-22.620222.52558.3438
31.33651.3507-1.77961.3094-2.17812.57370.21110.2065-0.2744-0.10150.0849-0.011-0.3262-0.3614-0.20960.88830.0738-0.01680.558-0.08610.6836-24.718833.6973-14.5325
41.6528-0.67360.16913.89091.48082.7761-0.10060.3019-0.13160.10710.0692-0.24960.4060.02770.01310.78870.01890.00870.6632-0.16440.6402-18.750547.2734-20.0488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 80 )A0 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 170 )A81 - 170
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 202 )A171 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 293 )A203 - 293

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