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- PDB-3sb2: Crystal Structure of the RNA chaperone Hfq from Herbaspirillum se... -

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Basic information

Entry
Database: PDB / ID: 3sb2
TitleCrystal Structure of the RNA chaperone Hfq from Herbaspirillum seropedicae SMR1
ComponentsProtein hfq
KeywordsCHAPERONE / Sm-like / RNA chaperone
Function / homology
Function and homology information


regulation of DNA-templated transcription / RNA binding
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesHerbaspirillum seropedicae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6301 Å
AuthorsKadowaki, M.A.S. / Iulek, J. / Barbosa, J.A.R.G. / Pedrosa, F.O. / Souza, E.M. / Chubatsu, L.S. / Monteiro, R.A. / Steffens, M.B.R.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Structural characterization of the RNA chaperone Hfq from the nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1.
Authors: Kadowaki, M.A. / Iulek, J. / Barbosa, J.A.R.G. / Pedrosa, F.D. / de Souza, E.M. / Chubatsu, L.S. / Monteiro, R.A. / de Oliveira, M.A. / Steffens, M.B.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 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)53,1817
Polymers53,0896
Non-polymers921
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-74 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.639, 65.323, 60.987
Angle α, β, γ (deg.)90.00, 105.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein hfq


Mass: 8848.127 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum seropedicae (bacteria) / Strain: SmR1 / Gene: hfq, Hsero_2948 / Plasmid: pKADO1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D8IZU6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M PCB pH 7.0 and 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.63→58.78 Å / Num. all: 13598 / Num. obs: 13212 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.02 % / Biso Wilson estimate: 59.911 Å2 / Rsym value: 0.045 / Net I/σ(I): 29.21
Reflection shellResolution: 2.63→2.7 Å / Redundancy: 5.78 % / Mean I/σ(I) obs: 6.52 / Rsym value: 0.302 / % possible all: 94.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6301→23.467 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic, but with TLS tensors. / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.83 / Stereochemistry target values: ML
Details: Each monomer was refined as a rigid group for TLS tensors. No non-crystallographic symmetry restraints were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 652 4.95 %RANDOM
Rwork0.1991 ---
all0.2029 13212 --
obs0.2029 13183 97.25 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.729 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.9452 Å20 Å24.2868 Å2
2---5.8032 Å20 Å2
3---12.7484 Å2
Refinement stepCycle: LAST / Resolution: 2.6301→23.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 6 158 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023088
X-RAY DIFFRACTIONf_angle_d0.5414221
X-RAY DIFFRACTIONf_dihedral_angle_d10.981088
X-RAY DIFFRACTIONf_chiral_restr0.036528
X-RAY DIFFRACTIONf_plane_restr0.002528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6301-2.83290.33081370.23952501X-RAY DIFFRACTION98
2.8329-3.11740.29251300.21582543X-RAY DIFFRACTION100
3.1174-3.56710.28031370.19942542X-RAY DIFFRACTION99
3.5671-4.4890.29141210.19612347X-RAY DIFFRACTION91
4.489-23.4680.22921270.1672598X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8983-0.57130.36551.2190.03820.7530.0173-0.1624-0.2380.03160.3630.15880.17430.0485-0.35360.14090.0022-0.06510.09820.02190.35016.8908-13.024233.2568
21.191-0.44310.39760.3271-0.13550.97840.1718-0.0829-0.36780.05170.02740.46220.36040.0203-0.18650.17330.0532-0.05030.09470.01270.317722.1819-17.22323.3302
30.2835-0.255-0.71762.0342-0.46342.4847-0.0915-0.19180.0154-0.1099-0.2269-0.73960.17410.6840.28390.14820.03420.08260.35290.07460.370227.6673-7.34758.8454
40.976-0.47180.5312.1645-0.46882.55880.07610.64360.24270.0639-0.1377-0.50140.25090.28330.09230.20430.0220.08070.40370.20590.267217.4368.49412.3512
54.14520.3552-0.42733.1023-0.44281.33630.7751.29820.92720.1948-0.1422-0.212-0.4222-0.1599-0.38710.2780.24270.14950.43120.31240.47641.069212.541611.4556
60.2271-0.4499-0.10331.35540.12580.3135-0.04440.21160.04440.0392-0.0540.3603-0.0762-0.17620.0760.12950.01660.02130.1520.0640.5451-4.47232.431227.0024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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