[English] 日本語
Yorodumi
- PDB-3b39: Structure of the DnaG primase catalytic domain bound to ssDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b39
TitleStructure of the DnaG primase catalytic domain bound to ssDNA
Components
  • DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')
  • DNA primasePrimase
Keywordstransferase/DNA / Protein-DNA complex / TOPRIM fold / DNA replication / DNA-directed RNA polymerase / Metal-binding / Nucleotidyltransferase / Primosome / Transcription / Transferase / Zinc-finger / transferase-DNA COMPLEX
Function / homology
Function and homology information


DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / replisome / DNA replication, synthesis of primer / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA binding ...DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / replisome / DNA replication, synthesis of primer / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 ...DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / Toprim-like / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA primase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCorn, J.E. / Pelton, J.G. / Berger, J.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Identification of a DNA primase template tracking site redefines the geometry of primer synthesis.
Authors: Corn, J.E. / Pelton, J.G. / Berger, J.M.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: 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
C: DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')
D: DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')
A: DNA primase
B: DNA primase


Theoretical massNumber of molelcules
Total (without water)81,7884
Polymers81,7884
Non-polymers00
Water2,630146
1
C: DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')
A: DNA primase


Theoretical massNumber of molelcules
Total (without water)40,8942
Polymers40,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')
B: DNA primase


Theoretical massNumber of molelcules
Total (without water)40,8942
Polymers40,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.829, 136.829, 71.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: DNA chain DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')


Mass: 4605.041 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA primase / Primase


Mass: 36288.969 Da / Num. of mol.: 2 / Fragment: RNA Polymerase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaG, dnaP, parB / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+
References: UniProt: P0ABS5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium acetate11
3sodium acetate11
4PEG 400012
5ammonium acetate12
6sodium acetate12

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.111 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 31918 / Num. obs: 30546 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3073 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDE

1dde


Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 19.362 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.447 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25443 1519 5.1 %RANDOM
Rwork0.21185 ---
obs0.21398 28547 94.63 %-
all-30166 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.878 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 240 0 146 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225337
X-RAY DIFFRACTIONr_bond_other_d0.0010.023623
X-RAY DIFFRACTIONr_angle_refined_deg1.1852.0257266
X-RAY DIFFRACTIONr_angle_other_deg0.94538748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81923.409264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44615851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9741554
X-RAY DIFFRACTIONr_chiral_restr0.0640.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
X-RAY DIFFRACTIONr_nbd_refined0.2130.21144
X-RAY DIFFRACTIONr_nbd_other0.2090.23782
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22563
X-RAY DIFFRACTIONr_nbtor_other0.0830.22821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.27
X-RAY DIFFRACTIONr_mcbond_it0.8071.53209
X-RAY DIFFRACTIONr_mcbond_other0.1261.51272
X-RAY DIFFRACTIONr_mcangle_it1.27424986
X-RAY DIFFRACTIONr_scbond_it1.77132486
X-RAY DIFFRACTIONr_scangle_it2.7244.52280
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 120 -
Rwork0.27 2169 -
obs--97.4 %
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)
12.98821.1339-0.67224.93710.7172.3863-0.1167-0.15240.0695-0.0810.079-0.00010.04690.22870.0377-0.0253-0.00420.0521-0.13630.0247-0.14-10.4059-29.2859-9.6126
24.63641.3427-1.94343.192-0.1862.2278-0.0257-0.1702-0.3695-0.1404-0.2122-0.1180.05490.09210.2379-0.0374-0.01730.0077-0.19680.0498-0.0567-25.7015-47.1002-1.8979
31.80341.2065-1.41793.8799-3.41229.30630.1297-0.50250.18530.1436-0.25120.2741-0.30040.00180.1216-0.0754-0.15820.0544-0.1061-0.0431-0.0477-43.141-52.910415.3496
43.57840.1254-0.5742.47050.34342.51740.16210.20540.1295-0.1635-0.0828-0.0264-0.15930.0949-0.0793-0.1163-0.0118-0.0026-0.01820.0043-0.127-25.7854-7.474212.5397
52.80060.42290.51393.66732.03382.70450.0140.1423-0.0727-0.0317-0.17770.144-0.0014-0.17710.1636-0.152-0.0095-0.0039-0.0606-0.0115-0.0991-47.1586-19.74648.1742
65.8157-0.56522.80685.5617-0.2397.68160.05920.5125-0.5743-0.5441-0.00610.64030.2002-0.4562-0.0531-0.1936-0.0749-0.06280.0716-0.16820.0742-57.263-35.2926-7.0674
724.728617.0622-3.266115.8159-8.772710.97580.6587-2.35520.11380.8612-1.3595-0.3772-0.65090.42970.70080.0169-0.03460.0187-0.11970.0292-0.1746-3.1585-22.78774.5793
82.255-1.6134-0.16941.52541.96299.1529-0.3667-1.0355-0.8275-0.7122-0.21830.5929-0.2054-0.6010.5850.0958-0.00780.008-0.18560.0470.0799-26.7824-8.7373-5.9687
90.0289-0.05870.02560.33130.13430.18630.0105-0.0426-0.0401-0.0648-0.02170.0556-0.0303-0.04420.0112-0.0575-0.02370.0082-0.04490.0043-0.0465-29.1724-26.16593.5549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC109 - 2392 - 132
2X-RAY DIFFRACTION2AC240 - 365133 - 258
3X-RAY DIFFRACTION3AC366 - 427259 - 320
4X-RAY DIFFRACTION4BD109 - 2392 - 132
5X-RAY DIFFRACTION5BD240 - 365133 - 258
6X-RAY DIFFRACTION6BD366 - 418259 - 311
7X-RAY DIFFRACTION7CA2 - 72 - 7
8X-RAY DIFFRACTION8DB3 - 113 - 10
9X-RAY DIFFRACTION9AE430 - 4911 - 62
10X-RAY DIFFRACTION9BF440 - 5061 - 67
11X-RAY DIFFRACTION9CG16 - 231 - 8
12X-RAY DIFFRACTION9DH95 - 1031 - 9

+
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://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