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- PDB-6lrb: The A form apo structure of NrS-1 C terminal region-CTR -

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Basic information

Entry
Database: PDB / ID: 6lrb
TitleThe A form apo structure of NrS-1 C terminal region-CTR
ComponentsPrimase
KeywordsHYDROLASE / primase / helicase / ssDNA-binding prorein
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
DNA Primase-polymerase
Similarity search - Component
Biological speciesNitratiruptor phage NrS-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsChen, X. / Gan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870721 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
DepositionJan 15, 2020Deposition 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 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
C: Primase
D: Primase
E: Primase
F: Primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,1968
Polymers290,1476
Non-polymers492
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27860 Å2
ΔGint-73 kcal/mol
Surface area97140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.719, 150.392, 149.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Primase /


Mass: 48357.855 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratiruptor phage NrS-1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: M5AAG8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8M Sodium acetate trihydrate pH 7.0

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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: May 24, 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, L10.382
11-L, -H, K20.354
11K, -L, -H30.264
ReflectionResolution: 2.6→30 Å / Num. obs: 103498 / % possible obs: 97.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.056 / Rrim(I) all: 0.152 / Χ2: 2.426 / Net I/σ(I): 6.9 / Num. measured all: 624268
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6430.43548180.0370.2720.5170.97592.7
2.64-2.693.40.4450190.0350.2590.5140.99395.3
2.69-2.743.60.4450050.0750.250.510.99296.2
2.74-2.83.70.44950800.0740.2510.5181.05196.8
2.8-2.863.80.44650470.1020.2450.5121.05596.6
2.86-2.933.90.4551100.0830.2420.5141.09597.6
2.93-34.10.44151450.1410.2330.5021.11497.6
3-3.084.30.43150890.1550.220.4871.18597.2
3.08-3.174.20.40851070.2040.2120.4631.19997.4
3.17-3.284.20.37651110.3590.1940.4271.24196.8
3.28-3.395.60.36251570.5610.1580.3971.34798.4
3.39-3.536.20.31651980.7980.1290.3431.46798.8
3.53-3.6970.27352400.8890.1040.2931.62799.1
3.69-3.887.50.21552530.9530.0780.2291.7699.1
3.88-4.1280.17752210.9730.0630.1881.93299.3
4.12-4.448.50.13153170.990.0450.1392.09799.1
4.44-4.898.10.10152500.9930.0350.1072.26199.1
4.89-5.599.90.09853580.9960.0310.1022.38199.6
5.59-7.039.90.08853730.9950.0280.0922.599.6
7.03-3010.40.06456000.9920.020.0688.60199.5

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K9C

6k9c


Resolution: 2.65→29.56 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.855 / SU B: 10.912 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.078
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 4723 5 %RANDOM
Rwork0.2332 ---
obs0.2377 89827 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 199.29 Å2 / Biso mean: 78.074 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--40.04 Å2-0 Å2-0 Å2
2--92.05 Å2-0 Å2
3----52 Å2
Refinement stepCycle: final / Resolution: 2.65→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19841 0 2 20 19863
Biso mean--28.27 29.18 -
Num. residues----2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0220236
X-RAY DIFFRACTIONr_bond_other_d0.0070.0219803
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.95927426
X-RAY DIFFRACTIONr_angle_other_deg1.177345603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84352440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.42225.667900
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.167153785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.531563
X-RAY DIFFRACTIONr_chiral_restr0.0840.23130
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222417
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024378
LS refinement shellResolution: 2.653→2.721 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 264 -
Rwork0.374 4468 -
all-4732 -
obs--66.09 %

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