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- PDB-8p9m: Hexameric Hfq from Chromobacterium haemolyticum -

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Basic information

Entry
Database: PDB / ID: 8p9m
TitleHexameric Hfq from Chromobacterium haemolyticum
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / Hfq / RNA-chaperon
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 / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesChromobacterium haemolyticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNikulin, A.D. / Lekontseva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation Russian Federation
CitationJournal: Crystallography Reports / Year: 2023
Title: The Structure of the Hfq Protein from Chromobacterium haemolyticum Revealed a New Variant of Regulation of RNA Binding with the Protein
Authors: Lekontseva, N.V. / Nikulin, A.D.
History
DepositionJun 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2337
Polymers58,1416
Non-polymers921
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-83 kcal/mol
Surface area19200 Å2
Unit cell
Length a, b, c (Å)58.505, 71.653, 96.652
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
RNA-binding protein Hfq


Mass: 9690.183 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium haemolyticum (bacteria)
Gene: hfq, B0T39_13335, B0T45_12055, CH06BL_33310, DBB33_18715
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W0CX06
#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.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG4000, 50 mM Tris-HCl, pH 7.5, 150 mM KCl, 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.33 Å / Num. obs: 27718 / % possible obs: 98.38 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Net I/σ(I): 8.19
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 5300 / CC1/2: 0.579 / Rpim(I) all: 0.76 / Rrim(I) all: 1.07 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.33 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1123 4.06 %
Rwork0.2224 --
obs0.2248 27674 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→22.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 6 248 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083356
X-RAY DIFFRACTIONf_angle_d0.9274569
X-RAY DIFFRACTIONf_dihedral_angle_d6.375435
X-RAY DIFFRACTIONf_chiral_restr0.058551
X-RAY DIFFRACTIONf_plane_restr0.008574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.35591500.32293285X-RAY DIFFRACTION100
2.09-2.20.32091380.27373316X-RAY DIFFRACTION100
2.2-2.340.36091610.2523302X-RAY DIFFRACTION100
2.34-2.520.31981370.25753321X-RAY DIFFRACTION100
2.52-2.770.34011310.26263335X-RAY DIFFRACTION99
2.77-3.170.36631220.24473327X-RAY DIFFRACTION99
3.17-3.990.24341400.19773340X-RAY DIFFRACTION98
3.99-22.330.21131440.17373325X-RAY DIFFRACTION94

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