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- PDB-6k9a: The complex of NrS-1 N terminal domain (1-305) with dGTP -

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Basic information

Entry
Database: PDB / ID: 6k9a
TitleThe complex of NrS-1 N terminal domain (1-305) with dGTP
ComponentsPrimase
KeywordsTRANSFERASE / primase / polymerase
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: 2.3 Å
AuthorsChen, X. / Gan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870721 China
CitationJournal: To Be Published
Title: Structural studies reveal a unique ring-shaped helicase architecture at the C-terminus of deep-sea vent phage DNA polymerase
Authors: Chen, X. / Gan, J.
History
DepositionJun 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4504
Polymers34,8621
Non-polymers5873
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.114, 58.007, 47.135
Angle α, β, γ (deg.)90.00, 92.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Primase


Mass: 34862.238 Da / Num. of mol.: 1 / Fragment: N terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratiruptor phage NrS-1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M5AAG8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4K

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Data collection

DiffractionMean temperature: 77.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14335 / % possible obs: 98.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.133 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1390 / Rrim(I) all: 0.367 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.739 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.38
RfactorNum. reflection% reflection
Rfree0.2477 702 4.95 %
Rwork0.2092 --
obs0.2112 14193 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 33 61 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022325
X-RAY DIFFRACTIONf_angle_d0.533146
X-RAY DIFFRACTIONf_dihedral_angle_d20.7831395
X-RAY DIFFRACTIONf_chiral_restr0.042326
X-RAY DIFFRACTIONf_plane_restr0.003401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47750.32621500.26522620X-RAY DIFFRACTION96
2.4775-2.72670.29441250.25932656X-RAY DIFFRACTION98
2.7267-3.12090.32371260.23732727X-RAY DIFFRACTION99
3.1209-3.93050.2391290.19552741X-RAY DIFFRACTION99
3.9305-29.74130.18961720.16952747X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.0631 Å / Origin y: 12.4183 Å / Origin z: 17.0698 Å
111213212223313233
T0.1709 Å2-0.0127 Å2-0.0212 Å2-0.2439 Å2-0.0899 Å2--0.2468 Å2
L0.1981 °2-0.3377 °2-0.0167 °2-2.0596 °2-0.419 °2--0.1431 °2
S0.0155 Å °0.0113 Å °0.0479 Å °-0.0917 Å °-0.0034 Å °0.1084 Å °-0.0399 Å °-0.0375 Å °-0.0131 Å °
Refinement TLS groupSelection details: all

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