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- PDB-1hk9: Crystal structure of the Hfq protein from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1hk9
TitleCrystal structure of the Hfq protein from Escherichia coli
ComponentsPROTEIN HFQ
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / SM-LIKE / PLEIOTROPIC REGULATOR / RNA CHAPERONE
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / 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
RNA-binding protein Hfq
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSauter, C. / Basquin, J. / Suck, D.
Citation
Journal: Nucleic Acids Res. / Year: 2003
Title: Sm-Like Proteins in Eubacteria: The Crystal Structure of the Hfq Protein from Escherichia Coli
Authors: Sauter, C. / Basquin, J. / Suck, D.
#1: Journal: Mol.Cell / Year: 2002
Title: The Sm-Like Hfq Protein Increases Oxys RNA Interaction with Target Mrnas
Authors: Zhang, A. / Wassarman, K.M. / Ortega, J. / Steven, A.C. / Storz, G.
#2: Journal: Mol.Cell / Year: 2002
Title: Hfq: A Bacterial Sm-Like Protein that Mediates RNA-RNA Interaction
Authors: Moller, T. / Franch, T. / Hojrup, P. / Keene, D.R. / Bachinger, H.P. / Brennan, R.G. / Valentin-Hansen, P.
#3: Journal: Embo J. / Year: 2002
Title: Structures of the Pleiotropic Translational Regulator Hfq and an Hfq-RNA Complex: A Bacterial Sm-Like Protein
Authors: Schumacher, M.A. / Pearson, R.F. / Moller, T. / Valentin-Hansen, P. / Brennan, R.G.
#4: Journal: Mol.Microbiol. / Year: 1994
Title: Characterization of Broadly Pleiotropic Phenotypes Caused by an Hfq Insertion Mutation in Escherichia Coli K-12
Authors: Tsui, H.C. / Leung, H.C. / Winkler, M.E.
#5: Journal: J.Biol.Chem. / Year: 1972
Title: Bacterial Proteins Required for Replication of Phage Q Ribonucleic Acid. Purification and Properties of Host Factor I, a Ribonucleic Acid-Binding Protein
Authors: De Fernandez, M.T.F. / Hayward, W.S. / August, J.T.
History
DepositionMar 6, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)49,5456
Polymers49,5456
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-73.7 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.350, 61.350, 166.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.49852, -0.86685, 0.00751), (0.86687, 0.49853, 0.00039), (-0.00409, 0.00631, 0.99997)3.18603, 0.70724, -0.32894
2given(-0.50046, -0.86556, -0.01888), (0.86449, -0.50078, 0.04318), (-0.04683, 0.00529, 0.99889)4.11841, 3.8005, 0.09246
3given(-0.99984, 0.00028, -0.01814), (-0.00042, -0.99997, 0.00786), (-0.01814, 0.00787, 0.9998)1.87618, 6.26372, 0.26117
4given(-0.50279, 0.86438, 0.00698), (-0.86431, -0.50259, -0.01934), (-0.01321, -0.01575, 0.99979)-1.28036, 5.4734, 0.62262
5given(-0.50279, 0.86438, 0.00698), (-0.86431, -0.50259, -0.01934), (-0.01321, -0.01575, 0.99979)-1.28036, 5.4734, 0.62262

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Components

#1: Protein
PROTEIN HFQ / HOST FACTOR-I PROTEIN / HF-1 / HF-I


Mass: 8257.572 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-72
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL RESIDUES 73-102 DELETED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6X3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRNA-BINDING PROTEIN THAT STIMULATES THE ELONGATION OF POLY(A) TAILS.EXISTS AS A HOMOHEXAMER. MAY ...RNA-BINDING PROTEIN THAT STIMULATES THE ELONGATION OF POLY(A) TAILS.EXISTS AS A HOMOHEXAMER. MAY FUNCTION TO DEGRADE SEVERAL MRNA'S BY INCREASING POLYADENYLATION.

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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: 1.83 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL SITTING DROPS. THE RESERVOIR CONTAINED 25% PEG 4000, 0.2 M NH4-ACETATE AND 0.2 M NA-ACETATE PH 4.6. CRYSTALLIZATION WERE CARRIED OUT AT 20C.
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 %PEG40001reservoir
30.2 Mammonium acetate1reservoir
40.2 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2002
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→47 Å / Num. obs: 19211 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.9
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.5 / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 47 Å / Num. obs: 19131 / % possible obs: 99.8 % / Num. measured all: 139736 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KQ1

1kq1


Resolution: 2.15→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2671995.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1615 8.4 %RANDOM
Rwork0.208 ---
obs0.208 19131 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.57 Å21.7 Å20 Å2
2---4.57 Å20 Å2
3---9.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 136 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it2.792.5
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.553.5
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.277 121 7.8 %
Rwork0.204 1436 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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