[English] 日本語
Yorodumi
- PDB-7qaz: Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qaz
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 / Prim-Pol / Primase-Polymerase / Primase / Polymerase / Complex
Function / homologyTetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / GTP binding / metal ion binding / : / Chem-DZ4 / GUANOSINE-5'-TRIPHOSPHATE / DNA / Uncharacterized protein
Function and homology information
Biological speciesMarinitoga sp. 1137 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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
DepositionNov 17, 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 / Category: struct_ref_seq_dif / Item: _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water7,116395
1
B: TPR_REGION domain-containing protein
D: Templating strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3059
Polymers28,5662
Non-polymers1,7397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TPR_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3743
Polymers25,8251
Non-polymers5492
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)227.910, 39.620, 79.770
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

-
Components

-
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)

-
Non-polymers , 4 types, 407 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.: 395 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.21 %
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 400uM 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 400uM DNA; 500uM AMPNPP; 4mM GTP; 2mM CoCl2; 130mM Monopotassium Glutamate

-
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: Aug 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.11→56.98 Å / Num. obs: 40376 / % possible obs: 94.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.36 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.085 / Rrim(I) all: 0.174 / Net I/σ(I): 6.5
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1427 / CC1/2: 0.298 / Rpim(I) all: 0.896 / Rrim(I) all: 1.382 / % possible all: 69.6

-
Processing

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

7nqe


Resolution: 2.11→56.98 Å / SU ML: 0.2847 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2608 1983 4.92 %
Rwork0.2097 38288 -
obs0.2123 40271 94.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.56 Å2
Refinement stepCycle: LAST / Resolution: 2.11→56.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 187 159 395 6179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735978
X-RAY DIFFRACTIONf_angle_d0.97878115
X-RAY DIFFRACTIONf_chiral_restr0.0565848
X-RAY DIFFRACTIONf_plane_restr0.0075992
X-RAY DIFFRACTIONf_dihedral_angle_d20.53512256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.3578950.33611994X-RAY DIFFRACTION69.7
2.16-2.220.41191040.31812233X-RAY DIFFRACTION77.67
2.22-2.290.32261260.29282365X-RAY DIFFRACTION83.62
2.29-2.360.31431320.28632643X-RAY DIFFRACTION92.47
2.36-2.440.33611290.27432846X-RAY DIFFRACTION98.94
2.44-2.540.31581410.24962868X-RAY DIFFRACTION99.7
2.54-2.660.28411550.24022874X-RAY DIFFRACTION99.61
2.66-2.80.27371540.22572840X-RAY DIFFRACTION99.34
2.8-2.970.28881740.22812857X-RAY DIFFRACTION99.7
2.97-3.20.25011360.20822890X-RAY DIFFRACTION99.38
3.2-3.530.25681400.19812920X-RAY DIFFRACTION99.74
3.53-4.040.23091570.17422929X-RAY DIFFRACTION99.07
4.04-5.080.2071570.15422934X-RAY DIFFRACTION99.01
5.08-56.980.23731830.19043095X-RAY DIFFRACTION99.12

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more