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- PDB-3qo3: Crystal structure of Escherichia coli Hfq, in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 3qo3
TitleCrystal structure of Escherichia coli Hfq, in complex with ATP
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / SM-LIKE / PLEIOTROPIC REGULATOR / RNA CHAPERONE / ATP-BINDING
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 / bacterial nucleoid / bent DNA binding / regulation of RNA stability / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / RNA folding chaperone / regulation of translation, ncRNA-mediated / bacterial nucleoid / bent DNA binding / regulation of RNA stability / tRNA processing / tRNA binding / regulation of DNA-templated transcription / DNA binding / RNA binding / ATP 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
ADENOSINE-5'-TRIPHOSPHATE / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBeich-Frandsen, M. / Vecerek, B. / Hammele, H. / Kloiber, K. / Sjoeblom, B. / Blasi, U. / Djinovic-Carugo, K.
CitationJournal: Plos One / Year: 2012
Title: Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq
Authors: Hammerle, H. / Beich-Frandsen, M. / Vecerek, B. / Rajkowitsch, L. / Carugo, O. / Djinovic-Carugo, K. / Blasi, U.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Protein hfq
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,98210
Polymers43,9536
Non-polymers2,0294
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-71 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.300, 40.620, 100.810
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein hfq / HF-1 / Host factor-I protein / HF-I


Mass: 7325.554 Da / Num. of mol.: 6 / Fragment: N-terminal (L)Sm core-domain, UNP residues 1-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4172, hfq, JW4130 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6X3
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 10% (W/V) PEG 8000, 8% (V/V) Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.15→98.67 Å / Num. all: 22913 / Num. obs: 21783 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 5.61 % / Biso Wilson estimate: 34.05 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.96
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 5.62 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1484 / % possible all: 88.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 2.15→19.89 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.967 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25727 1167 5.1 %RANDOM
Rwork0.2279 ---
all0.2294 22913 --
obs0.2294 21689 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.687 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.04 Å2
2--1.55 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 124 244 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223114
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2192.0254252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6595360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86724.545132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58315546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5111518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212240
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1541.51836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96923018
X-RAY DIFFRACTIONr_scbond_it3.08531278
X-RAY DIFFRACTIONr_scangle_it4.3164.51234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 79 -
Rwork0.287 1586 -
obs--100 %

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