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- PDB-4ou7: Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a nove... -

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Basic information

Entry
Database: PDB / ID: 4ou7
TitleCrystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode
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 / DNA unwinding involved in DNA replication / protein homotrimerization / DNA-templated DNA replication / single-stranded DNA binding / magnesium ion binding / identical protein binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1180 / Primosomal protein 1 / DnaT, DNA-binding domain / DnaT DNA-binding domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Primosomal protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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
S: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)43,8396
Polymers43,8396
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.408, 46.689, 54.392
Angle α, β, γ (deg.)87.33, 86.01, 70.20
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
11SERSERAA84 - 1541 - 71
21SERSERBB84 - 1541 - 71
12ARGARGAA84 - 1521 - 69
22ARGARGCC84 - 1521 - 69
13SERSERAA84 - 1541 - 71
23SERSERDD84 - 1541 - 71
14SERSERAA84 - 1541 - 71
24SERSEREE84 - 1541 - 71
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: 8168.346 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 84-154
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

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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: 2.52 Å3/Da / Density % sol: 51.24 %
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: 1.54 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.83→38.02 Å / Num. obs: 9917

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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: 2.83→38.02 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23827 475 4.8 %RANDOM
Rwork0.18349 ---
obs0.18611 9443 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.241 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å2-2.98 Å20.51 Å2
2--1.18 Å2-2.16 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.83→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 200 0 0 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193198
X-RAY DIFFRACTIONr_bond_other_d00.022921
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.8594388
X-RAY DIFFRACTIONr_angle_other_deg3.44936690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1855349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67623.103145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57415464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1491520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213463
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9056.741411
X-RAY DIFFRACTIONr_mcbond_other3.9026.7361410
X-RAY DIFFRACTIONr_mcangle_it6.00810.0941755
X-RAY DIFFRACTIONr_mcangle_other6.71910.141756
X-RAY DIFFRACTIONr_scbond_it4.4237.6681787
X-RAY DIFFRACTIONr_scbond_other5.0767.4711786
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.71411.1022634
X-RAY DIFFRACTIONr_long_range_B_refined10.82157.5323786
X-RAY DIFFRACTIONr_long_range_B_other10.81957.5213785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35400.13
12B35400.13
21A34680.15
22C34680.15
31A34870.16
32D34870.16
41A34690.16
42E34690.16
51B37350.1
52C37350.1
61B37570.1
62D37570.1
71B37930.12
72E37930.12
81C36780.1
82D36780.1
91C36590.12
92E36590.12
101D37400.12
102E37400.12
LS refinement shellResolution: 2.825→2.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 28 -
Rwork0.238 669 -
obs--91.47 %

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