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- PDB-1kq1: 1.55 A Crystal structure of the pleiotropic translational regulat... -

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Basic information

Entry
Database: PDB / ID: 1kq1
Title1.55 A Crystal structure of the pleiotropic translational regulator, Hfq
ComponentsHost Factor for Q beta
KeywordsTRANSLATION / Hfq / hexamer / RNA binding protein / translational regulator / Sm motif
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / 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
ACETIC ACID / RNA-binding protein Hfq / RNA-binding protein Hfq
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.55 Å
AuthorsSchumacher, M.A. / Pearson, R.F. / Moller, T. / Valentin-Hansen, P. / Brennan, R.G.
CitationJournal: 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.
History
DepositionJan 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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: Host Factor for Q beta
B: Host Factor for Q beta
H: Host Factor for Q beta
I: Host Factor for Q beta
K: Host Factor for Q beta
M: Host Factor for Q beta
S: Host Factor for Q beta
T: Host Factor for Q beta
Y: Host Factor for Q beta
N: Host Factor for Q beta
R: Host Factor for Q beta
W: Host Factor for Q beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,74017
Polymers105,44012
Non-polymers3005
Water10,665592
1
A: Host Factor for Q beta
B: Host Factor for Q beta
H: Host Factor for Q beta
I: Host Factor for Q beta
K: Host Factor for Q beta
M: Host Factor for Q beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9009
Polymers52,7206
Non-polymers1803
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-44 kcal/mol
Surface area18100 Å2
MethodPISA
2
S: Host Factor for Q beta
T: Host Factor for Q beta
Y: Host Factor for Q beta
N: Host Factor for Q beta
R: Host Factor for Q beta
W: Host Factor for Q beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8408
Polymers52,7206
Non-polymers1202
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-52 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.030, 89.950, 67.770
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number4
Space group name H-MP1211
DetailsHfq forms a hexamer (resistant to denaturants) and there are two hexamers in the crystallographic asymmetric unit

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Components

#1: Protein
Host Factor for Q beta / Hfq


Mass: 8786.683 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q99UG9, UniProt: A0A0H3JV59*PLUS
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 35.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1150 mM11NaCl
225 mMTris11pH7.5
30.5 mMEDTA11
420 mg/mlHfq11
52.5 Mammonium sulfate12
60.4 Macetic acid12pH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.55→22.37 Å / Num. obs: 115018 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 7.6
Reflection shellResolution: 1.55→1.65 Å / Rsym value: 0.158 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 22.4 Å / Num. obs: 111857 / Num. measured all: 460147 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Lowest resolution: 1.6 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
PHASESphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIR / Resolution: 1.55→22.37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1029855.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
Details: residues 67 to 77 are disordered in all subunits as are residues 1-5 in 11 subunits.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5801 5 %RANDOM
Rwork0.237 ---
obs-115018 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3442 Å2 / ksol: 0.46278 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å23.42 Å2
2---0.04 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.55→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5999 0 0 612 6611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 1029 5.4 %
Rwork0.34 18109 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ACY_PAR.TXTACY_TOP.TXT
Refinement
*PLUS
Lowest resolution: 22.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.374 / Rfactor Rwork: 0.34

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