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- PDB-7nqe: Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinit... -

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Basic information

Entry
Database: PDB / ID: 7nqe
TitlePrim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 with dGTP
ComponentsTPR_REGION domain-containing protein
KeywordsTRANSFERASE / AEP Archaeo-Eukaryotic Primase Apo Prim-Pol Primase-Polymerase Primase Polymerase
Function / homologyTetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Uncharacterized protein
Function and homology information
Biological speciesMarinitoga sp. 1137 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsLi, A.W.H. / Doherty, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S008691/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M008800/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P007031/1 United Kingdom
CitationJournal: Nature / Year: 2022
Title: Molecular basis for the initiation of DNA primer synthesis.
Authors: Li, A.W.H. / Zabrady, K. / Bainbridge, L.J. / Zabrady, M. / Naseem-Khan, S. / Berger, M.B. / Kolesar, P. / Cisneros, G.A. / Doherty, A.J.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 25, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity_src_gen / struct / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title / _struct_ref_seq_dif.details
Revision 1.3Jun 8, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,24911
Polymers26,1971
Non-polymers1,05210
Water3,495194
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint7 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.953, 62.675, 82.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein TPR_REGION domain-containing protein


Mass: 26197.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinitoga sp. 1137 (bacteria) / Strain: DSM 14283 / JCM 11233 / KA3 / Gene: Marpi_0402 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2J4R1
#2: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium Thiocyanate 20% PEG 3350 10mM MnCl2 2mM dGTP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.28→62.68 Å / Num. obs: 53746 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 14.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.036 / Rrim(I) all: 0.088 / Net I/σ(I): 9.6
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 1 / Num. unique obs: 2412 / CC1/2: 0.284 / Rpim(I) all: 0.956 / Rrim(I) all: 1.914 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NQD

7nqd


Resolution: 1.28→49.9 Å / SU ML: 0.1778 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 2636 4.92 %
Rwork0.1629 50933 -
obs0.1643 53569 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.76 Å2
Refinement stepCycle: LAST / Resolution: 1.28→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 61 194 2068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562022
X-RAY DIFFRACTIONf_angle_d1.00722731
X-RAY DIFFRACTIONf_chiral_restr0.0881283
X-RAY DIFFRACTIONf_plane_restr0.0067354
X-RAY DIFFRACTIONf_dihedral_angle_d6.7307275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.37571120.32592383X-RAY DIFFRACTION88.85
1.3-1.330.37531280.30352566X-RAY DIFFRACTION95.16
1.33-1.360.34431390.2692601X-RAY DIFFRACTION98.49
1.36-1.380.30671140.23622637X-RAY DIFFRACTION97.69
1.38-1.420.24871360.20952659X-RAY DIFFRACTION99.75
1.42-1.450.21841270.18812695X-RAY DIFFRACTION99.51
1.45-1.490.22171370.17432677X-RAY DIFFRACTION99.54
1.49-1.540.21121260.16872696X-RAY DIFFRACTION99.93
1.54-1.590.20161610.1662676X-RAY DIFFRACTION99.79
1.59-1.640.18461350.162652X-RAY DIFFRACTION99.89
1.64-1.710.20361400.15332679X-RAY DIFFRACTION99.93
1.71-1.790.20291320.14982727X-RAY DIFFRACTION99.97
1.79-1.880.16851520.1442693X-RAY DIFFRACTION99.89
1.88-20.19221240.13992736X-RAY DIFFRACTION100
2-2.150.15341740.14332678X-RAY DIFFRACTION100
2.15-2.370.1771560.14532727X-RAY DIFFRACTION100
2.37-2.710.19311410.16142748X-RAY DIFFRACTION100
2.71-3.410.17891550.1562769X-RAY DIFFRACTION100
3.42-49.90.17031470.15782934X-RAY DIFFRACTION100

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