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- PDB-7p9j: Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinit... -

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Basic information

Entry
Database: PDB / ID: 7p9j
TitlePrim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 - Primer Initiation Complex
Components
  • TPR_REGION domain-containing protein
  • Templating strand
KeywordsTRANSFERASE / AEP Archaeo-Eukaryotic Primase Apo Prim-Pol Primase-Polymerase Primase Polymerase
Function / homology
Function and homology information


GTP binding / metal ion binding
Similarity search - Function
: / TOTE conflict system, Archaeo-Eukaryotic Primase domain / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / Chem-DZ4 / GUANOSINE-5'-TRIPHOSPHATE / DNA / TOTE conflict system primase domain-containing protein
Similarity search - Component
Biological speciesMarinitoga sp. 1137 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJul 27, 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 / Structure summary / Category: struct / struct_ref_seq_dif / Item: _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 1.4Nov 2, 2022Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Jan 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
B: TPR_REGION domain-containing protein
C: TPR_REGION domain-containing protein
D: Templating strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,11116
Polymers80,2154
Non-polymers2,89612
Water2,774154
1
B: TPR_REGION domain-containing protein
D: Templating strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2468
Polymers28,5662
Non-polymers1,6806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4334
Polymers25,8251
Non-polymers6083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4334
Polymers25,8251
Non-polymers6083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)227.820, 39.500, 74.980
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

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein TPR_REGION domain-containing protein


Mass: 25824.678 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinitoga sp. 1137 (bacteria) / Gene: Marpi_0402 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: H2J4R1
#2: DNA chain Templating strand


Mass: 2740.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 166 molecules

#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium HEPES; MOPS (acid) 20% v/v Ethylene glycol; 10% w/v PEG 8000 0.03M Diethylene glycol; 0.03M Triethylene glycol; 0.03M Tetraethylene glycol; 0.03M Pentaethylene glycol 200uM DNA; ...Details: 0.1M Sodium HEPES; MOPS (acid) 20% v/v Ethylene glycol; 10% w/v PEG 8000 0.03M Diethylene glycol; 0.03M Triethylene glycol; 0.03M Tetraethylene glycol; 0.03M Pentaethylene glycol 200uM DNA; 500uM AMPNPP; 2mM GTP; 2mM CoCl2; 140mM Monopotassium Glutamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→45.35 Å / Num. obs: 41762 / % possible obs: 76.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 37.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.051 / Rrim(I) all: 0.087 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.373 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2100 / CC1/2: 0.282 / Rpim(I) all: 1.112 / Rrim(I) all: 1.777 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia23.4.2data reduction
XSCALEdata scaling
PHASER2.8.3phasing
Coot0.9.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NQD

7nqd


Resolution: 1.9→45.35 Å / SU ML: 0.3492 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 2145 5.15 %
Rwork0.2275 39494 -
obs0.2291 41639 76.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 120 159 154 5797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00945794
X-RAY DIFFRACTIONf_angle_d1.3477856
X-RAY DIFFRACTIONf_chiral_restr0.0775830
X-RAY DIFFRACTIONf_plane_restr0.0081966
X-RAY DIFFRACTIONf_dihedral_angle_d19.55452159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.47381550.43712631X-RAY DIFFRACTION77.93
1.94-1.990.33481520.3792707X-RAY DIFFRACTION79.44
1.99-2.050.39911490.34992654X-RAY DIFFRACTION79.14
2.05-2.110.38561460.32762720X-RAY DIFFRACTION79.32
2.11-2.170.31861470.29472685X-RAY DIFFRACTION78.45
2.18-2.250.32941560.27282662X-RAY DIFFRACTION79.09
2.25-2.340.27991450.26562681X-RAY DIFFRACTION78.11
2.34-2.450.3431440.2592639X-RAY DIFFRACTION77.35
2.45-2.580.28321300.25662661X-RAY DIFFRACTION77.04
2.58-2.740.26281350.24452635X-RAY DIFFRACTION76.54
2.74-2.950.25651510.23312589X-RAY DIFFRACTION75.44
2.95-3.250.24691320.22342591X-RAY DIFFRACTION73.89
3.25-3.720.22741430.19862526X-RAY DIFFRACTION72.7
3.72-4.680.21081310.17452559X-RAY DIFFRACTION72
4.69-45.350.22261290.19582554X-RAY DIFFRACTION68.23

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