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- PDB-6k9c: The apo structure of NrS-1 C terminal region (305-718) -

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Basic information

Entry
Database: PDB / ID: 6k9c
TitleThe apo structure of NrS-1 C terminal region (305-718)
ComponentsPrimase
KeywordsTRANSFERASE / primase / helicase / ssDNA-binding protein
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 / SAD / Resolution: 2.406 Å
AuthorsChen, X. / Gan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870721 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural studies reveal a ring-shaped architecture of deep-sea vent phage NrS-1 polymerase.
Authors: Chen, X. / Su, S. / Chen, Y. / Gao, Y. / Li, Y. / Shao, Z. / Zhang, Y. / Shao, Q. / Liu, H. / Li, J. / Ma, J. / Gan, J.
History
DepositionJun 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 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
B: Primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5979
Polymers96,7162
Non-polymers8817
Water1,36976
1
A: Primase
B: Primase
hetero molecules

A: Primase
B: Primase
hetero molecules

A: Primase
B: Primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,79227
Polymers290,1476
Non-polymers2,64421
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area30600 Å2
ΔGint-503 kcal/mol
Surface area98740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.130, 161.130, 161.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Primase


Mass: 48357.855 Da / Num. of mol.: 2
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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.6 M NaH2PO4/0.4 M K2HPO4, 0.1 M phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 54069 / % possible obs: 99.7 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.09 / Net I/σ(I): 21.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2622 / Rrim(I) all: 0.545 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.406→29.921 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.2408 2433 4.9 %
Rwork0.1929 --
obs0.1952 49645 91.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.406→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6709 0 27 76 6812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066865
X-RAY DIFFRACTIONf_angle_d0.8469306
X-RAY DIFFRACTIONf_dihedral_angle_d20.0114138
X-RAY DIFFRACTIONf_chiral_restr0.0551058
X-RAY DIFFRACTIONf_plane_restr0.0071161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4057-2.45480.3854470.35751123X-RAY DIFFRACTION37
2.4548-2.50820.3366940.3031725X-RAY DIFFRACTION58
2.5082-2.56650.35461670.29322273X-RAY DIFFRACTION77
2.5665-2.63060.36341310.28332748X-RAY DIFFRACTION91
2.6306-2.70170.3081490.27572890X-RAY DIFFRACTION96
2.7017-2.78110.29341390.2573008X-RAY DIFFRACTION99
2.7811-2.87080.30941590.25322912X-RAY DIFFRACTION99
2.8708-2.97340.27251360.23653055X-RAY DIFFRACTION100
2.9734-3.09230.30611540.21653002X-RAY DIFFRACTION100
3.0923-3.23290.24941790.20922995X-RAY DIFFRACTION100
3.2329-3.40310.25181710.20063044X-RAY DIFFRACTION100
3.4031-3.6160.23551560.17433021X-RAY DIFFRACTION100
3.616-3.89460.23061180.15923055X-RAY DIFFRACTION100
3.8946-4.28550.20321390.14673065X-RAY DIFFRACTION100
4.2855-4.90330.181580.12893057X-RAY DIFFRACTION100
4.9033-6.16880.19851710.16013066X-RAY DIFFRACTION100
6.1688-29.92340.16481650.15443173X-RAY DIFFRACTION100
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)
10.6767-0.1631-0.42293.71250.92561.4839-0.03940.19750.0128-0.04390.0143-0.0972-0.06990.10330.00230.22580.0050.04760.22740.06670.2444132.000251.653498.2223
21.9331-0.1531-0.73511.2659-0.31861.6130.017-0.1232-0.10650.06350.08160.10710.0735-0.1551-0.11510.2021-0.04170.02280.21210.09290.1487109.441973.5009109.0548
33.12180.28160.05552.40160.0563.1634-0.1140.03940.5974-0.00810.0276-0.1237-0.47640.03540.05890.2474-0.0187-0.05230.13840.01030.1834104.487593.6057147.7708
41.57820.8557-0.72612.93362.23843.19210.05230.09980.34350.10480.1651-0.6081-0.070.4015-0.19990.29230.0503-0.06580.29990.05260.4782146.753748.6005117.2983
51.86070.1052-0.06712.12060.57381.67010.14990.0403-0.0724-0.1988-0.0495-0.159-0.2046-0.0497-0.11130.26190.0198-0.02570.29240.09510.2117132.747974.583132.3453
62.14440.19370.00372.74670.66331.62210.0302-0.12980.05410.0481-0.01080.0486-0.04510.0560.00910.1432-0.0008-0.07150.2254-0.03840.1081109.747877.3167168.646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 303:391)
2X-RAY DIFFRACTION2(chain A and resseq 392:617)
3X-RAY DIFFRACTION3(chain A and resseq 618:718)
4X-RAY DIFFRACTION4(chain B and resseq 305:391)
5X-RAY DIFFRACTION5(chain B and resseq 392:617)
6X-RAY DIFFRACTION6(chain B and resseq 618:718)

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