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- PDB-5uk7: Escherichia coli Hfq bound to dsDNA -

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Basic information

Entry
Database: PDB / ID: 5uk7
TitleEscherichia coli Hfq bound to dsDNA
Components
  • DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')
  • RNA-binding protein Hfq
KeywordsDNA BINDING PROTEIN/DNA / RNA-binding protein / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / RNA folding chaperone / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA-binding protein Hfq / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOrans, J. / Kovach, A.R. / Brennan, R.G.
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli Hfq DNA complex reveals multifunctional nucleic acid binding site
Authors: Orans, J. / Kovach, A.R. / Hoff, K.E. / Brennan, R.G.
History
DepositionJan 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
N: DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')
M: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')
Y: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')
Z: DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,93528
Polymers116,15016
Non-polymers78512
Water2,108117
1
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
N: DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')
M: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,46814
Polymers58,0758
Non-polymers3926
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
hetero molecules

Y: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')
Z: DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)58,46814
Polymers58,0758
Non-polymers3926
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Unit cell
Length a, b, c (Å)65.749, 65.795, 81.996
Angle α, β, γ (deg.)105.930, 92.280, 119.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RNA-binding protein Hfq


Mass: 7634.875 Da / Num. of mol.: 12 / Fragment: UNP residues 2-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hfq, A6I92_23385, AWG90_11910, HMPREF3040_03060 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A148HSM9, UniProt: P0A6X3*PLUS
#2: DNA chain DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')


Mass: 6187.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')


Mass: 6078.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28-38% MPD, 0.1 M Tris pH 7.5-8.5 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18997 / % possible obs: 83.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 43.11 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.794 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
3-3.051.50.351.36153.1
3.05-3.111.60.2981.185160.1
3.11-3.171.60.3231.647159.6
3.17-3.231.60.2111.678167.6
3.23-3.31.70.1871.446172.4
3.3-3.381.70.3011.502175.5
3.38-3.461.80.3051.509180.3
3.46-3.561.80.2461.51183.6
3.56-3.661.90.2722.51188.7
3.66-3.781.90.2142.591188.1
3.78-3.911.90.191.74191.3
3.91-4.071.90.1771.6192.3
4.07-4.261.90.1441.661194
4.26-4.481.90.0982.11193.2
4.48-4.761.90.0821.918193.8
4.76-5.1320.0841.806195.3
5.13-5.6420.1031.629196.8
5.64-6.4620.0921.778197.3
6.46-8.1320.0711.757197.8
8.13-501.90.0291.925195.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.1_1168refinement
CNSrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GIB

3gib


Resolution: 3→25.685 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.44
RfactorNum. reflection% reflection
Rfree0.2598 1060 5.02 %
Rwork0.2105 --
obs0.2129 18997 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.32 Å2 / Biso mean: 55.29 Å2 / Biso min: 19.61 Å2
Refinement stepCycle: final / Resolution: 3→25.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 1640 12 117 8044
Biso mean--35.05 40.11 -
Num. residues----872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068227
X-RAY DIFFRACTIONf_angle_d1.13111477
X-RAY DIFFRACTIONf_chiral_restr0.0681351
X-RAY DIFFRACTIONf_plane_restr0.0061182
X-RAY DIFFRACTIONf_dihedral_angle_d21.5563214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.13650.2791080.23422009211776
3.1365-3.30150.28911230.2482271239486
3.3015-3.50790.29691200.23792547266796
3.5079-3.77790.26831260.21622658278499
3.7779-4.15670.29811560.225926442800100
4.1567-4.75490.22861460.176526412787100
4.7549-5.97820.26991370.206726802817100
5.9782-25.68590.21611440.19812591273599

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