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- PDB-1u1t: Hfq protein from Pseudomonas aeruginosa. High-salt crystals -

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Basic information

Entry
Database: PDB / ID: 1u1t
TitleHfq protein from Pseudomonas aeruginosa. High-salt crystals
ComponentsHfq protein
KeywordsRNA BINDING PROTEIN / Hfq / HF1 / Sm-like bacterial protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of carbon utilization / regulation of RNA stability / quorum sensing / regulation of translation / 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
RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNikulin, A.D. / Stolboushkina, E.A. / Perederina, A.A. / Vassilieva, I.M. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. ...Nikulin, A.D. / Stolboushkina, E.A. / Perederina, A.A. / Vassilieva, I.M. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S.V. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Pseudomonas aeruginosa Hfq protein.
Authors: Nikulin, A. / Stolboushkina, E. / Perederina, A. / Vassilieva, I. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hfq protein
B: Hfq protein
C: Hfq protein
D: Hfq protein
E: Hfq protein
F: Hfq protein


Theoretical massNumber of molelcules
Total (without water)54,6876
Polymers54,6876
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-77 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 72.350, 109.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hfq protein


Mass: 9114.487 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hfq / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9HUM0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 M Li2SO4, 0.6 M ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 40524 / Num. obs: 40524 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.8 / Num. unique all: 9200 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 1.9→24.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3567365.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1878 4.9 %RANDOM
Rwork0.205 ---
all0.222 39911 --
obs0.205 38033 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1183 Å2 / ksol: 0.371734 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.24 Å20 Å20 Å2
2--1.79 Å20 Å2
3---8.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 164 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.341.5
X-RAY DIFFRACTIONc_mcangle_it6.42
X-RAY DIFFRACTIONc_scbond_it7.072
X-RAY DIFFRACTIONc_scangle_it9.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 315 5.1 %
Rwork0.329 5817 -
obs-5817 95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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