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- PDB-3hsb: Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex... -

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Basic information

Entry
Database: PDB / ID: 3hsb
TitleCrystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer
Components
  • Protein hfq
  • RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / Sm-like motif / Protein-RNA complex / RNA-binding / Stress response / RNA BINDING PROTEIN-RNA COMPLEX
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
RNA / RNA-binding protein Hfq
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaba, S. / Someya, T. / Kumasaka, T. / Kawai, G. / Nakamura, K.
Citation
Journal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq
Authors: Someya, T. / Baba, S. / Fujimoto, M. / Kawai, G. / Kumasaka, T. / Nakamura, K.
#1: Journal: To be Published
Title: Expression, crystallization and preliminary crystallographic analysis of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.
Authors: Baba, S. / Someya, T. / Kumasaka, T. / Kawai, G. / Nakamura, K.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
X: RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)55,9137
Polymers55,9137
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-46 kcal/mol
Surface area19070 Å2
Unit cell
Length a, b, c (Å)123.700, 123.700, 119.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein
Protein hfq


Mass: 8934.214 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ymaH / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O31796
#2: RNA chain RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3')


Mass: 2307.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Sequence of an RNA aptamer for Protein Hfq.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.015 M Cobalt (II) chloride hexahydrate, 0.1 M MES monohydrate, 1.8 M Ammonium sulfate, 119 uM RNA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 5, 2008 / Details: Toroidal Mirror
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 23732 / Num. obs: 23732 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.8 % / Rmerge(I) obs: 0.063 / Rsym value: 0.042 / Net I/σ(I): 38.02
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 7.07 / Num. unique all: 2309 / Rsym value: 0.291 / % possible all: 9.72

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KQ2

1kq2


Resolution: 2.2→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2310 -RANDOM
Rwork0.214 ---
obs0.214 23224 97.9 %-
all-23732 --
Solvent computationBsol: 52.753 Å2
Displacement parametersBiso max: 68.55 Å2 / Biso mean: 33.353 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.086 Å20 Å20 Å2
2---1.086 Å20 Å2
3---2.172 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 154 0 138 3619
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5761.5
X-RAY DIFFRACTIONc_scbond_it2.1222
X-RAY DIFFRACTIONc_mcangle_it2.5232
X-RAY DIFFRACTIONc_scangle_it3.232.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4GOL.param
X-RAY DIFFRACTION5dna-rna_rep.param

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