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- PDB-3qsu: Structure of Staphylococcus aureus Hfq in complex with A7 RNA -

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Basic information

Entry
Database: PDB / ID: 3qsu
TitleStructure of Staphylococcus aureus Hfq in complex with A7 RNA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA chaperone Hfq
KeywordsCHAPERONE/RNA / hexamer / Sm/Lsm family / RNA chaperone / translational regulator / mRNA / sRNA / cytoplasma / CHAPERONE-RNA complex
Function / homologySH3 type barrels. - #100 / SH3 type barrels. / Roll / Mainly Beta / RNA / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrennan, R. / Horstmann, N. / Link, T.M.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.
Authors: Horstmann, N. / Orans, J. / Valentin-Hansen, P. / Shelburne, S.A. / Brennan, R.G.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Jun 19, 2013Group: Derived calculations
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_auth_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA chaperone Hfq
B: RNA chaperone Hfq
H: RNA chaperone Hfq
I: RNA chaperone Hfq
K: RNA chaperone Hfq
M: RNA chaperone Hfq
C: RNA chaperone Hfq
D: RNA chaperone Hfq
E: RNA chaperone Hfq
F: RNA chaperone Hfq
G: RNA chaperone Hfq
J: RNA chaperone Hfq
N: RNA chaperone Hfq
S: RNA chaperone Hfq
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,42945
Polymers127,53316
Non-polymers1,89729
Water3,729207
1
A: RNA chaperone Hfq
B: RNA chaperone Hfq
H: RNA chaperone Hfq
I: RNA chaperone Hfq
K: RNA chaperone Hfq
M: RNA chaperone Hfq
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,76419
Polymers54,9807
Non-polymers78512
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA chaperone Hfq
D: RNA chaperone Hfq
E: RNA chaperone Hfq
F: RNA chaperone Hfq
G: RNA chaperone Hfq
J: RNA chaperone Hfq
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,83020
Polymers54,9807
Non-polymers85013
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
N: RNA chaperone Hfq
S: RNA chaperone Hfq
hetero molecules

N: RNA chaperone Hfq
S: RNA chaperone Hfq
hetero molecules

N: RNA chaperone Hfq
S: RNA chaperone Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,50518
Polymers52,7206
Non-polymers78512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8880 Å2
ΔGint-415 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.397, 156.397, 34.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
RNA chaperone Hfq


Mass: 8786.683 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: subsp. aureus ECT-R 2 / Gene: ECTR2_1161, hfq / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / References: UniProt: E5RBT2
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2259.483 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12 % MPD, 0.1 M Na-cacodylate, 0.2 M Zn(0Ac)2, 0.1M KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Na-cacodylate11
3Zn(0Ac)211
4KCl11
5MPD12
6Na-cacodylate12
7Zn(0Ac)212
8KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.2→78.2 Å / Num. all: 48116 / Num. obs: 47823 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.34 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→78.198 Å / SU ML: 0.27 / σ(F): 0.01 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1937 4.25 %
Rwork0.1956 --
obs0.1981 45560 94.7 %
all-47819 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.419 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.6153 Å20 Å20 Å2
2---13.6153 Å2-0 Å2
3---27.2307 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.2→78.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 176 29 207 7325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087249
X-RAY DIFFRACTIONf_angle_d1.0099814
X-RAY DIFFRACTIONf_dihedral_angle_d18.2542628
X-RAY DIFFRACTIONf_chiral_restr0.0721101
X-RAY DIFFRACTIONf_plane_restr0.0031224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27870.28321750.23424005X-RAY DIFFRACTION87
2.2787-2.36990.30311840.20944118X-RAY DIFFRACTION89
2.3699-2.47780.33151860.22524181X-RAY DIFFRACTION90
2.4778-2.60840.2741910.23544269X-RAY DIFFRACTION94
2.6084-2.77190.28051990.21214376X-RAY DIFFRACTION95
2.7719-2.98590.26922010.19494475X-RAY DIFFRACTION98
2.9859-3.28640.24682020.19044583X-RAY DIFFRACTION99
3.2864-3.76190.25582030.18674581X-RAY DIFFRACTION99
3.7619-4.73950.22822050.16624593X-RAY DIFFRACTION100
4.7395-78.24790.24161910.20694442X-RAY DIFFRACTION96

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