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- PDB-6k9b: Apo structure of NrS-1 N terminal domain N305 -

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Basic information

Entry
Database: PDB / ID: 6k9b
TitleApo structure of NrS-1 N terminal domain N305
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-directed DNA polymerase / DNA helicase / 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 / Resolution: 2.45 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Primase
B: Primase


Theoretical massNumber of molelcules
Total (without water)69,7242
Polymers69,7242
Non-polymers00
Water28816
1
A: Primase


Theoretical massNumber of molelcules
Total (without water)34,8621
Polymers34,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Primase


Theoretical massNumber of molelcules
Total (without water)34,8621
Polymers34,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.136, 107.555, 66.868
Angle α, β, γ (deg.)90.00, 113.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 0 - 292 / Label seq-ID: 1 - 293

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Primase


Mass: 34862.238 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-tris pH 6.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11-H, -K, H+L20.498
ReflectionResolution: 2.45→30 Å / Num. obs: 24723 / % possible obs: 97.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.134 / Net I/σ(I): 10.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2338 / Rrim(I) all: 0.438 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→29.52 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.288 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23167 1133 5 %RANDOM
Rwork0.18805 ---
obs0.19025 21573 89.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å2-0 Å20.08 Å2
2--4.97 Å20 Å2
3----3.03 Å2
Refinement stepCycle: 1 / Resolution: 2.45→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 0 16 4476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194566
X-RAY DIFFRACTIONr_bond_other_d0.0020.024254
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9596168
X-RAY DIFFRACTIONr_angle_other_deg1.02939838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6724.091220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04315802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6191532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215120
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021024
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2354.3162224
X-RAY DIFFRACTIONr_mcbond_other1.2334.3152223
X-RAY DIFFRACTIONr_mcangle_it2.1696.4672772
X-RAY DIFFRACTIONr_mcangle_other2.1696.4682773
X-RAY DIFFRACTIONr_scbond_it1.0124.4512342
X-RAY DIFFRACTIONr_scbond_other1.0124.4522343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.786.6243397
X-RAY DIFFRACTIONr_long_range_B_refined3.4233.4824934
X-RAY DIFFRACTIONr_long_range_B_other3.4233.4914935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 32766 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.448→2.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 59 -
Rwork0.24 895 -
obs--51.54 %

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