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

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Basic information

Entry
Database: PDB / ID: 3ahu
TitleCrystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.
Components
  • 5'-R(*AP*GP*AP*GP*AP*G)-3'
  • Protein hfq
KeywordsTRANSLATION/RNA / Sm-like motif / Protein-RNA complex / TRANSLATION-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: To be Published
Title: Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.
Authors: Someya, T. / Baba, S. / Fujimoto, M. / Kumasaka, T. / Kawai, G. / Nakamura, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.
Authors: Baba, S. / Someya, T. / Kawai, G. / Nakamura, K. / Kumasaka, T.
History
DepositionApr 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Protein hfq
B: Protein hfq
C: Protein hfq
X: 5'-R(*AP*GP*AP*GP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)28,7814
Polymers28,7814
Non-polymers00
Water45025
1
A: Protein hfq
B: Protein hfq
C: Protein hfq

A: Protein hfq
B: Protein hfq
C: Protein hfq
X: 5'-R(*AP*GP*AP*GP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)55,5847
Polymers55,5847
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
crystal symmetry operation2_455-x-1,-y,z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.921, 92.504, 114.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Protein hfq


Mass: 8934.214 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU17340, hfq, ymaH / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O31796
#2: RNA chain 5'-R(*AP*GP*AP*GP*AP*G)-3'


Mass: 1978.277 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01M cobalt (II) chloride, 0.2M MES, 1.8M ammonium sulfate, 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: Oct 17, 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→30 Å / Num. all: 12626 / Num. obs: 12626 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.033 / Rsym value: 0.029 / Net I/σ(I): 45.75
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.84 / Num. unique all: 1219 / Rsym value: 0.248 / % possible all: 100

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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: 1KQ2

1kq2


Resolution: 2.2→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1225 -RANDOM
Rwork0.2592 ---
obs0.2592 12044 95.4 %-
all-12626 --
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 132 0 25 1786

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