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

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Basic information

Entry
Database: PDB / ID: 7nqf
TitlePrim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 with dsDNA
Components
  • DNA(CGTGDG)
  • TPR_REGION domain-containing protein
KeywordsTRANSFERASE / AEP Archaeo-Eukaryotic Primase Apo Prim-Pol Primase-Polymerase Primase Polymerase
Function / homology: / TOTE conflict system, Archaeo-Eukaryotic Primase domain / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / GTP binding / metal ion binding / : / DNA / TOTE conflict system primase domain-containing protein
Function and homology information
Biological speciesMarinitoga sp. 1137 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 ...entity_src_gen / struct / struct_ref / struct_ref_seq / 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.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
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

Downloads & links

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Assembly

Deposited unit
A: TPR_REGION domain-containing protein
B: TPR_REGION domain-containing protein
C: DNA(CGTGDG)
D: DNA(CGTGDG)
E: DNA(CGTGDG)
F: DNA(CGTGDG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,21210
Polymers58,9766
Non-polymers2364
Water3,063170
1
A: TPR_REGION domain-containing protein
C: DNA(CGTGDG)
D: DNA(CGTGDG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6065
Polymers29,4883
Non-polymers1182
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPR_REGION domain-containing protein
E: DNA(CGTGDG)
F: DNA(CGTGDG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6065
Polymers29,4883
Non-polymers1182
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.041, 160.362, 39.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein TPR_REGION domain-containing protein


Mass: 25837.697 Da / Num. of mol.: 2
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: DNA chain
DNA(CGTGDG)


Mass: 1825.216 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Sodium cacodylate PEG 4000 Sodium Chloride Spermine Cobalt chloride Guanosine triphosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.02→80.18 Å / Num. obs: 33089 / % possible obs: 99.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 34.34 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.086 / Rrim(I) all: 0.182 / Net I/σ(I): 5.6
Reflection shellResolution: 2.02→2.06 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.986 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1622 / CC1/2: 0.321 / Rpim(I) all: 1.059 / Rrim(I) all: 2.257 / % possible all: 99.9

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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: 2.02→69.44 Å / SU ML: 0.3356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.837
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2593 1557 4.73 %
Rwork0.2121 31375 -
obs0.2144 32932 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.23 Å2
Refinement stepCycle: LAST / Resolution: 2.02→69.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 484 4 170 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084253
X-RAY DIFFRACTIONf_angle_d0.94235822
X-RAY DIFFRACTIONf_chiral_restr0.056623
X-RAY DIFFRACTIONf_plane_restr0.0079670
X-RAY DIFFRACTIONf_dihedral_angle_d19.7678716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.090.4071320.35982720X-RAY DIFFRACTION96.51
2.09-2.160.42651520.32662752X-RAY DIFFRACTION99.38
2.16-2.250.34271500.28262805X-RAY DIFFRACTION99.39
2.25-2.350.29141380.25392857X-RAY DIFFRACTION99.83
2.35-2.480.28631360.25142818X-RAY DIFFRACTION99.76
2.48-2.630.26441390.24012850X-RAY DIFFRACTION99.53
2.63-2.830.35821360.2222835X-RAY DIFFRACTION99.7
2.83-3.120.30191450.21872853X-RAY DIFFRACTION99.9
3.12-3.570.2471330.19092903X-RAY DIFFRACTION99.9
3.57-4.50.18771380.16422906X-RAY DIFFRACTION99.54
4.5-69.440.21811580.18943076X-RAY DIFFRACTION99.72
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)
10.06710611079410.0453663753508-0.04451362675540.01231787297290.003716933934390.0575619144958-0.133002939639-0.58267911541-0.1231264160230.155312313790.364301965970.02797943976890.77925125313-0.449713973447-1.0047738454E-70.4416564967240.0845797034710.001964477751150.3870501347380.03490643561680.349352307035-42.307843962525.1917312878-3.89756019355
20.1143382019060.1543686922170.1475437365540.02331274868920.1106025128510.164723880491-0.04611662411240.1411080073220.185082559841-0.104252813248-0.336120191885-0.050677748812-0.1013516924280.03550569497261.46462252231E-70.324069340535-0.02057688556270.003036189501650.2383258371740.02454706937160.394650701354-5.629713254129.04966869641-17.3567489388
30.074121130766-0.01932090902770.09389639265760.139998428544-0.04818564831660.0473936214043-0.021650602085-0.3548505042760.53227964349-0.350609784649-0.3060011438920.2489287412650.03364372385370.0567751269-9.53160670868E-70.292855779304-0.01897114376040.02889888835150.2215918068670.01981333375560.36217820071-2.4260551002410.2945631901-12.1898500007
40.0216608350805-0.01694227592340.05931043087080.0153185718992-0.0233250581882-0.0258539199395-0.705442479851-0.421649775195-1.18426648899-0.265356504368-0.283045764555-0.110484192506-0.6987918431660.8528048994052.52977392038E-6-0.929437410785-1.34043053622-0.607969079632-0.497981352762-0.1168018318430.778032357851-27.022917807453.3755184671-15.2260555441
50.02430071075980.02764937106870.0133485796795-0.00265175696331-0.03554936789890.0583231406015-0.0633152707066-0.3772605752920.2313659748860.2021277471520.4935566985310.0713021899679-0.7613729864261.313240325541.94432066241E-60.553078787120.124785124088-0.2050458637140.968585463832-0.1587640969010.884912876433-30.886216573751.1879177833-9.48244652303
60.05430121921410.06440678620230.04101511443650.0267898787212-0.002322016097230.000467339357349-0.08753129035090.186118566662-0.055264850657-0.2165213358080.065250789930.2593171201770.186899655501-0.1174178106099.80263992613E-80.298899040183-0.06126939952320.01353968753560.222477453923-0.02204382806530.319680330533-27.680465566-11.8318154518-12.9730673293
70.674670235822-0.290746011976-0.3850610884150.539050710330.02824252081440.104333951257-0.0104275938656-0.00278045462906-0.404573548866-0.0598151932127-0.0271280052586-0.145212635901-0.0602174703118-0.0054399939814-4.87781476394E-90.2252374529510.006738201818120.02434042779350.2126618832110.01489895224520.335873339763-13.6533826846-8.01268297295-14.0480174174
8-0.25891039778-0.257766501476-0.007740915347890.445120761364-0.2915478805680.217747737546-0.1255430627420.0511389768540.06001126356490.0456005838683-0.0258519444107-0.06876816293260.02613672554680.13941037311-3.95554578327E-80.2366263842890.00100512416663-0.02800395772240.28840949661-0.04673820474330.187485851898-16.67834359829.68727241797-8.85859409218
90.1610860496810.13369006623-0.2237342723490.0601861666991-0.08378994695770.0830129819595-0.02208965167820.01105588413940.07420848917990.0616067592735-0.0323409100676-0.02611491434880.0619950645540.0111785281504-1.25813855813E-60.2308995490910.00599384196024-0.0274229060280.2549970180320.003862487201830.173624422198-26.319651787115.9887599921-2.76198767442
100.134350855784-0.137404379101-0.01272645543420.6499139219150.5126817156780.623421632353-0.0040204290580.0324290546798-0.08130459778530.0413640940106-0.0282987498299-0.0943349165613-0.00623108056208-0.0533157424789-1.15686892056E-70.198075346658-0.0316100597147-0.02668718742780.2335294094230.02625833487120.2288079618-25.61764271859.015521436-15.1349363311
11-0.154858971099-0.118735101453-0.385346830973-0.05238611716320.05204783006990.0441277851237-0.03262937094050.04470254526920.111997735007-0.112119279485-0.0003588661712980.00739642722436-0.220611065540.1578155871324.68467552296E-70.2588765365570.00603362380076-0.01830484302250.237914100831-0.02166736572740.237282219637-16.464550694312.4711064471-15.0679943032
120.1815396833760.293662386074-0.2954828780910.8201749924670.07654116668450.9924203576790.002395132671390.0755228630269-0.2129652510670.102924393771-0.00143451448630.1679247067670.035992244756-0.0482002991723-3.75023406164E-80.18874551678-0.02693894084260.002772304439640.198783398010.005636706783650.2100008959-27.26068751893.36374350027-11.1965774583
130.0448044301350.0219837354298-0.0647590127968-0.00827843152959-0.01974905708690.00570827172057-0.06306923932960.34121639983-0.4847220147870.626286212458-0.1058626821990.315832137069-0.236944297595-0.2162953058816.99521327356E-70.1884959322360.0247978718140.05420620259360.416679580172-0.05063761387780.35126402919-57.994002788142.3621121713-23.8495426098
140.286864361288-0.1732478101340.2351738041880.5504125400670.560249382638-0.2674356385340.0282768360326-0.09213294989970.1052303762330.002436083100640.0589001882388-0.001085797496-0.149230066736-0.207749723232-1.39679547659E-80.271343071570.04111738486090.002209866896620.2629679604130.003061732246720.298713851197-48.366713083553.0500048132-19.2117033348
150.624749169623-0.263646984333-0.1667201957950.154012239214-0.354282455-0.0862713083231-0.0359755647923-0.0002653830846530.07920218148090.1025257716270.0804184299092-0.1105753568090.0292910853510.06989195758994.09248120669E-80.2290947349560.00668092292171-0.006751458663870.287656989825-0.03687616301620.26268225097-32.808980195936.7524502298-22.9146640906
160.222827898896-0.159944707124-0.4777626103310.151405114385-0.06763940311060.255625842559-0.0624129794556-0.00750397533628-0.05050880791730.05383894935770.0375103813994-0.129211302317-0.122993738370.0427291117671.01054262652E-80.2642641420370.0376994564511-0.0009676942686160.2787517365420.008120878860570.252603454383-37.546629412434.5838538639-16.85750984
171.04454467132-0.16561452734-0.2811580658630.335047430883-0.006894451087990.141665306373-0.03385272937570.1033257795640.0978084398822-0.097975636645-0.0898063344140.0179689344851-0.01360157505780.02451807108411.36284100197E-70.2780387734960.0333363453284-0.04371945416570.226747788768-0.01448340508210.221911386062-41.723779116543.0359515535-23.6125042116
18-0.124157306527-0.05441464728310.02958621269010.005114037187610.08335310452790.08022825199960.192412922170.0578567778106-0.1392715786750.1425224381430.06553680616760.328380370725-0.006625302199-0.320771546554-9.00315948049E-70.2604640160870.027552850469-0.06168744897330.359524768552-0.04103866944990.264024803329-52.971753557833.5137061295-24.2984731616
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 315 through 328 )BD315 - 328206 - 219
22chain 'C' and (resid 1 through 6 )CG1 - 6
33chain 'D' and (resid 1 through 6 )DH1 - 6
44chain 'E' and (resid 1 through 6 )EI1 - 6
55chain 'F' and (resid 1 through 6 )FJ1 - 6
66chain 'A' and (resid 111 through 122 )AA111 - 1221 - 12
77chain 'A' and (resid 123 through 165 )AA123 - 16513 - 55
88chain 'A' and (resid 166 through 189 )AA166 - 18956 - 79
99chain 'A' and (resid 190 through 210 )AA190 - 21080 - 100
1010chain 'A' and (resid 211 through 250 )AA211 - 250101 - 140
1111chain 'A' and (resid 251 through 272 )AA251 - 272141 - 162
1212chain 'A' and (resid 273 through 328 )AA273 - 328163 - 218
1313chain 'B' and (resid 110 through 122 )BD110 - 1221 - 13
1414chain 'B' and (resid 123 through 164 )BD123 - 16414 - 55
1515chain 'B' and (resid 165 through 210 )BD165 - 21056 - 101
1616chain 'B' and (resid 211 through 262 )BD211 - 262102 - 153
1717chain 'B' and (resid 263 through 302 )BD263 - 302154 - 193
1818chain 'B' and (resid 303 through 314 )BD303 - 314194 - 205

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