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- PDB-6bdg: HFQ monomer in spacegroup p6 at 1.93 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6bdg
TitleHFQ monomer in spacegroup p6 at 1.93 angstrom resolution
ComponentsRNA-binding protein Hfq
KeywordsCHAPERONE / RNA binding chaperone
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-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.964 Å
AuthorsBrown, C. / Zhang, K. / Seo, C. / Ellis, M.J. / Hanniford, D.B. / Junop, M.
CitationJournal: To Be Published
Title: HFQ monomer in spacegroup p6 at 1.93 angstrom resolution
Authors: Ellis, M.J. / Brown, C. / Zhang, K. / Seo, C. / Junop, M. / Hanniford, D.B.
History
DepositionOct 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

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Assembly

Deposited unit
A: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)7,3011
Polymers7,3011
Non-polymers00
Water73941
1
A: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)43,8036
Polymers43,8036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area8530 Å2
ΔGint-73 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.370, 61.370, 28.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein RNA-binding protein Hfq


Mass: 7300.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: hfq, ECS88_4758 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MKX6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na/K phosphate pH 6.2 10 % W/V PEG 3000 10 mM Spermidine 5 mM Mg Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→19.36 Å / Num. obs: 4191 / % possible obs: 94 % / Redundancy: 2 % / CC1/2: 0.991 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9644→2.2483 Å / Redundancy: 1.9 % / CC1/2: 0.862 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.964→19.359 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2327 424 10.12 %
Rwork0.1917 --
obs0.1961 4189 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.964→19.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 0 41 555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007524
X-RAY DIFFRACTIONf_angle_d1.065711
X-RAY DIFFRACTIONf_dihedral_angle_d13.982198
X-RAY DIFFRACTIONf_chiral_restr0.03885
X-RAY DIFFRACTIONf_plane_restr0.00690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9644-2.24830.24741350.20731239X-RAY DIFFRACTION94
2.2483-2.83130.27641350.21481221X-RAY DIFFRACTION97
2.8313-19.36020.20721540.17481305X-RAY DIFFRACTION96

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