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- PDB-6gwk: The crystal structure of Hfq from Caulobacter crescentus -

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Basic information

Entry
Database: PDB / ID: 6gwk
TitleThe crystal structure of Hfq from Caulobacter crescentus
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / Hfq / Caulobacter / sRNA / RNA-protein interactions / natively unstructured protein
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 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSantiago-Frangos, A. / Frohlich, K.S. / Jeliazkov, J.R. / Gray, J.R. / Luisi, B.F. / Woodson, S.A. / Hardwick, S.W.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Wellcome Trust200873/Z/16/Z United Kingdom
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R01 GM120425 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Caulobacter crescentusHfq structure reveals a conserved mechanism of RNA annealing regulation.
Authors: Santiago-Frangos, A. / Frohlich, K.S. / Jeliazkov, J.R. / Malecka, E.M. / Marino, G. / Gray, J.J. / Luisi, B.F. / Woodson, S.A. / Hardwick, S.W.
History
DepositionJun 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 30, 2022Group: Advisory / Author supporting evidence / Database references
Category: database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
M: RNA-binding protein Hfq
N: RNA-binding protein Hfq
O: RNA-binding protein Hfq
P: RNA-binding protein Hfq
Q: RNA-binding protein Hfq
R: RNA-binding protein Hfq
S: RNA-binding protein Hfq
T: RNA-binding protein Hfq
U: RNA-binding protein Hfq
V: RNA-binding protein Hfq
W: RNA-binding protein Hfq
X: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)222,03824
Polymers222,03824
Non-polymers00
Water1,982110
1
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


Theoretical massNumber of molelcules
Total (without water)55,5096
Polymers55,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-77 kcal/mol
Surface area19100 Å2
MethodPISA
2
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)55,5096
Polymers55,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-79 kcal/mol
Surface area18420 Å2
MethodPISA
3
M: RNA-binding protein Hfq
N: RNA-binding protein Hfq
O: RNA-binding protein Hfq
P: RNA-binding protein Hfq
Q: RNA-binding protein Hfq
R: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)55,5096
Polymers55,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-78 kcal/mol
Surface area19100 Å2
MethodPISA
4
S: RNA-binding protein Hfq
T: RNA-binding protein Hfq
U: RNA-binding protein Hfq
V: RNA-binding protein Hfq
W: RNA-binding protein Hfq
X: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)55,5096
Polymers55,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-73 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.322, 97.322, 203.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein ...
RNA-binding protein Hfq


Mass: 9251.575 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 / Gene: hfq, CC_1745 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A7H8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium thiocyanate, 17 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→87.81 Å / Num. obs: 100169 / % possible obs: 97.42 % / Redundancy: 2 % / Biso Wilson estimate: 36.75 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1228 / Rpim(I) all: 0.0923 / Rrim(I) all: 0.1548 / Net I/σ(I): 9.44
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.6281 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 10091 / CC1/2: 0.618 / Rpim(I) all: 0.5247 / Rrim(I) all: 0.823 / % possible all: 99.06

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Processing

Software
NameVersionClassification
DIALSdata collection
PHENIXdev_3112refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNO

4pno


Resolution: 2.15→87.81 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 42.2779
RfactorNum. reflection% reflection
Rfree0.3051 4990 4.98 %
Rwork0.2783 --
obs0.2797 100169 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→87.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12737 0 0 110 12847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002813073
X-RAY DIFFRACTIONf_angle_d0.519917832
X-RAY DIFFRACTIONf_chiral_restr0.04292153
X-RAY DIFFRACTIONf_plane_restr0.0032254
X-RAY DIFFRACTIONf_dihedral_angle_d6.66959030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.44852520.43874775X-RAY DIFFRACTION94.52
2.19-2.230.40012760.37844780X-RAY DIFFRACTION93.25
2.23-2.270.44042560.38114772X-RAY DIFFRACTION93.33
2.27-2.320.33482320.35844765X-RAY DIFFRACTION92.98
2.32-2.370.32742550.34754793X-RAY DIFFRACTION93.47
2.37-2.420.40162180.35914861X-RAY DIFFRACTION95.59
2.42-2.480.34692340.35054843X-RAY DIFFRACTION94.96
2.48-2.550.33152610.34114776X-RAY DIFFRACTION93.63
2.55-2.620.31272460.33154867X-RAY DIFFRACTION94.91
2.62-2.710.36762210.34654862X-RAY DIFFRACTION95
2.71-2.810.34012740.34794695X-RAY DIFFRACTION92.09
2.81-2.920.37742550.32914603X-RAY DIFFRACTION90.52
2.92-3.050.36052440.29584884X-RAY DIFFRACTION94.36
3.05-3.210.31432590.28774783X-RAY DIFFRACTION94.02
3.21-3.410.3112340.27194790X-RAY DIFFRACTION93.9
3.41-3.670.27712320.24644746X-RAY DIFFRACTION93
3.67-4.040.28032550.24854641X-RAY DIFFRACTION89.68
4.04-4.630.24272600.20024740X-RAY DIFFRACTION92.27
4.63-5.820.2532640.2114576X-RAY DIFFRACTION89.34
5.82-29.270.26062620.24054575X-RAY DIFFRACTION88.34

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