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

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Basic information

Entry
Database: PDB / ID: 7nqd
TitlePrim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137
ComponentsTPR_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 / TOTE conflict system primase domain-containing protein
Function and homology information
Biological speciesMarinitoga sp. 1137 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 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 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)52,3942
Polymers52,3942
Non-polymers00
Water00
1
A: TPR_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,1971
Polymers26,1971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPR_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,1971
Polymers26,1971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.380, 97.380, 109.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 113 through 115 or (resid 116...
d_2ens_1(chain "B" and ((resid 113 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSA1 - 70
d_12ens_1GLUGLUA73 - 207
d_21ens_1GLNVALB1 - 165
d_22ens_1LYSGLUB172 - 211

NCS oper: (Code: givenMatrix: (0.161212573714, -0.949905996525, 0.267748209783), (-0.904488166652, -0.250749387892, -0.345001305589), (0.394856508701, -0.186556538982, -0.899602687468)Vector: 40. ...NCS oper: (Code: given
Matrix: (0.161212573714, -0.949905996525, 0.267748209783), (-0.904488166652, -0.250749387892, -0.345001305589), (0.394856508701, -0.186556538982, -0.899602687468)
Vector: 40.70324216, 44.8386932147, -25.7551095737)

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Components

#1: Protein TPR_REGION domain-containing protein


Mass: 26197.076 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

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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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M PCTP 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.97→45.79 Å / Num. obs: 12181 / % possible obs: 100 % / Redundancy: 6.75 % / Biso Wilson estimate: 79.5 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.09 / Rrim(I) all: 0.237 / Net I/σ(I): 8.5
Reflection shellResolution: 2.97→3.02 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.752 / Num. unique obs: 605 / CC1/2: 0.3 / Rpim(I) all: 0.717 / Rrim(I) all: 1.896 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
xia2data scaling
SHELXDEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.97→45.79 Å / SU ML: 0.4397 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 604 4.97 %
Rwork0.216 11558 -
obs0.2172 12162 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.09 Å2
Refinement stepCycle: LAST / Resolution: 2.97→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 0 0 3361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263428
X-RAY DIFFRACTIONf_angle_d0.61964625
X-RAY DIFFRACTIONf_chiral_restr0.0472508
X-RAY DIFFRACTIONf_plane_restr0.0041600
X-RAY DIFFRACTIONf_dihedral_angle_d15.28391244
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.932048685477 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.270.34011590.30012862X-RAY DIFFRACTION99.83
3.27-3.740.29271620.25262866X-RAY DIFFRACTION99.8
3.74-4.710.23891580.20362878X-RAY DIFFRACTION100
4.71-45.790.18571250.19092952X-RAY DIFFRACTION99.9
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)
10.7452871315620.6681780219470.561868963560.7161046069890.201652098111.23730638375-0.0531599050449-0.236822521270.4026086246130.0564188554482-0.13919783521-0.334191906691-0.0293463890689-0.425879464188-6.63422583805E-50.5084179842270.00669276590373-0.004063204724540.5325951746760.01285615742150.56732509796625.011459143926.87731662968.89429588392
20.9287044328320.2593859545890.6601661601080.855979926875-0.31002841070.288341981639-0.182622473721-0.136620366994-0.409613915953-0.1164451348780.1281213750990.06898878328950.02797750060750.0974628211513.01834651201E-60.5754623618350.004275697987050.009488324883450.564442711415-0.02781460886880.53416874760323.67119443865.52782694338.57490786259
30.78166776088-0.7331965301190.2626931050712.250319128570.1617992725210.974603289554-0.009860772553150.01239724864370.0302511399587-0.1610667529270.0299863200562-0.1827314458440.03497352893190.06339331224962.68967551149E-50.609871639745-0.04719769014870.03536082500130.5501964420380.01675572385720.53385135469327.188801108810.54129215389.89738483719
40.0423556020319-0.1708853181470.08198411656870.02046174802720.003544529691160.0674334756614-0.718787672236-0.132092319164-1.405572903380.7993839170580.1254592171270.5751810983080.5089939289230.592571991949-0.08904981727240.687869266690.1157184266890.131653130760.709446141951-0.08839451238520.86644433678325.0473755976.17487175647-30.538691532
50.7487128261270.160756526648-0.219816920640.6187583337290.3896792525430.3583170991720.001194380365080.0380931061351-0.0566402778432-0.184447397411-0.001452577043550.3743179686410.00900894993354-0.286393479808-0.004361495999230.5656343168630.03692383559660.04622270571340.774879379729-0.018674422750.63415846859920.496579258314.6064595215-28.3348847271
60.4266214971340.0935506209583-0.1818511111541.037986226430.6314041642960.5826290701140.115269327450.1411063635260.236163652855-0.265340075221-0.358403831982-0.2802762109450.1717527112740.1535346856731.88029473934E-50.5631950925890.02417947512570.1079119137680.5820256039280.002110948532680.79622653151341.260320885918.8293959141-25.0481771387
7-0.01483210299890.032059644161-0.002322791026010.0138765854573-0.01184678230370.164060535522-0.1621887900260.104866235490.3245259881450.136068548511-0.148676887211-1.26498218472-0.5154174496080.0679855561648-0.0002108910303280.568369622066-0.03468035656110.05380274009410.532617263905-0.1224074305181.3038965778942.319679388526.132403058-21.5596016734
80.7583549823440.6310101791110.5326517135341.493676832510.3727817127050.338889080026-0.100569258643-0.3370512210460.43900160883-0.092566323884-0.154236554036-0.2395654231310.1391095286550.58051321858-0.0002272202459840.5942783798840.107312071720.1260069126950.707836077460.04188129316520.61228245188831.677498442718.5662500989-30.3590393451
90.387712207182-0.2253327913880.1453859633590.2488818503280.03240073458220.06534639250170.01117911177790.151486079161-0.3431552210280.107933818102-0.257339619246-0.29585589590.3885896899690.8640129404240.0005360451345620.7185257265850.06624916659490.1223275850720.716418409919-0.06105693250660.69291547873141.64240137845.83719808312-22.0696189917
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 113 through 172 )AA113 - 1721 - 60
22chain 'A' and (resid 173 through 250 )AA173 - 25061 - 135
33chain 'A' and (resid 251 through 328 )AA251 - 328136 - 207
44chain 'B' and (resid 113 through 129 )BB113 - 1291 - 17
55chain 'B' and (resid 130 through 172 )BB130 - 17218 - 60
66chain 'B' and (resid 173 through 250 )BB173 - 25061 - 133
77chain 'B' and (resid 251 through 262 )BB251 - 262134 - 145
88chain 'B' and (resid 263 through 302 )BB263 - 302146 - 185
99chain 'B' and (resid 303 through 330 )BB303 - 330186 - 213

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