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- PDB-4ou6: Crystal structure of DnaT84-153-dT10 ssDNA complex form 1 -

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Basic information

Entry
Database: PDB / ID: 4ou6
TitleCrystal structure of DnaT84-153-dT10 ssDNA complex form 1
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Primosomal protein 1
KeywordsREPLICATION/DNA / DNA binding / REPLICATION-DNA complex
Function / homology
Function and homology information


DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / DNA replication, synthesis of primer / replication fork processing / protein homotrimerization / : / DNA-templated DNA replication / single-stranded DNA binding / magnesium ion binding / identical protein binding
Similarity search - Function
Primosomal protein 1 / DnaT, DNA-binding domain / DnaT DNA-binding domain
Similarity search - Domain/homology
DNA / Primosomal protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLiu, Z. / Chen, P. / Niu, L. / Teng, M. / Li, X.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode.
Authors: Liu, Z. / Chen, P. / Wang, X. / Cai, G. / Niu, L. / Teng, M. / Li, X.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Primosomal protein 1
B: Primosomal protein 1
C: Primosomal protein 1
D: Primosomal protein 1
E: Primosomal protein 1
L: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)46,0316
Polymers46,0316
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.144, 47.416, 54.135
Angle α, β, γ (deg.)88.34, 86.25, 71.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA84 - 1531 - 70
21ALAALABB84 - 1531 - 70
12ARGARGAA84 - 1521 - 69
22ARGARGCC84 - 1521 - 69
13ALAALAAA84 - 1531 - 70
23ALAALADD84 - 1531 - 70
14ALAALAAA84 - 1531 - 70
24ALAALAEE84 - 1531 - 70
15ARGARGBB84 - 1521 - 69
25ARGARGCC84 - 1521 - 69
16SERSERBB84 - 1541 - 71
26SERSERDD84 - 1541 - 71
17SERSERBB84 - 1541 - 71
27SERSEREE84 - 1541 - 71
18ARGARGCC84 - 1521 - 69
28ARGARGDD84 - 1521 - 69
19ARGARGCC84 - 1521 - 69
29ARGARGEE84 - 1521 - 69
110SERSERDD84 - 1541 - 71
210SERSEREE84 - 1541 - 71

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Primosomal protein 1 / Primosomal protein I


Mass: 8606.826 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 84-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaT, b4362, JW4326 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8J2
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2996.971 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.96→27.54 Å / Num. obs: 30764

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→27.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.458 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22846 1559 5.1 %RANDOM
Rwork0.1886 ---
obs0.19056 29206 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-1.65 Å21.05 Å2
2--1.97 Å2-1.62 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 1.96→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 200 0 257 3372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193230
X-RAY DIFFRACTIONr_bond_other_d0.0070.022951
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.8624432
X-RAY DIFFRACTIONr_angle_other_deg1.25636760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8565354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1423.151146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08815467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2891520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213505
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02795
X-RAY DIFFRACTIONr_mcbond_it2.4883.7871431
X-RAY DIFFRACTIONr_mcbond_other2.4843.7841430
X-RAY DIFFRACTIONr_mcangle_it3.695.651780
X-RAY DIFFRACTIONr_mcangle_other3.695.6541781
X-RAY DIFFRACTIONr_scbond_it3.0594.6211799
X-RAY DIFFRACTIONr_scbond_other3.0564.6171798
X-RAY DIFFRACTIONr_scangle_other4.8056.8662653
X-RAY DIFFRACTIONr_long_range_B_refined7.43834.9884075
X-RAY DIFFRACTIONr_long_range_B_other7.23634.6383962
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A37590.12
12B37590.12
21A37310.12
22C37310.12
31A35940.14
32D35940.14
41A36860.14
42E36860.14
51B37850.1
52C37850.1
61B38060.11
62D38060.11
71B38820.1
72E38820.1
81C36580.12
82D36580.12
91C37650.1
92E37650.1
101D37820.11
102E37820.11
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 109 -
Rwork0.214 2051 -
obs--92.27 %

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