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- PDB-3hfn: Crystal Structure of an Hfq protein from Anabaena sp. -

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Basic information

Entry
Database: PDB / ID: 3hfn
TitleCrystal Structure of an Hfq protein from Anabaena sp.
ComponentsAsl2047 protein
KeywordsRNA BINDING PROTEIN / HFQ / SM / RNA-BINDING PROTEIN / SRNA / TRANSLATIONAL REGULATION
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 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsBoggild, A. / Overgaard, M. / Valentin-Hansen, P. / Brodersen, D.E.
CitationJournal: Febs J. / Year: 2009
Title: Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties.
Authors: Boggild, A. / Overgaard, M. / Valentin-Hansen, P. / Brodersen, D.E.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asl2047 protein
B: Asl2047 protein


Theoretical massNumber of molelcules
Total (without water)16,0122
Polymers16,0122
Non-polymers00
Water00
1
A: Asl2047 protein
B: Asl2047 protein

A: Asl2047 protein
B: Asl2047 protein

A: Asl2047 protein
B: Asl2047 protein


Theoretical massNumber of molelcules
Total (without water)48,0376
Polymers48,0376
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8730 Å2
ΔGint-31 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.580, 60.580, 32.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 8 - 70 / Label seq-ID: 9 - 71

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Asl2047 protein


Mass: 8006.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: codons optimised for E. coli expression / Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: asl2047 / Plasmid: pTYP11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q8YVD1

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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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 2 M ammonium sulphate, 0.1 M citric acid, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2008
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.085
11-H, H+K, -L20.455
11K, H, -L30.46
ReflectionResolution: 2.3→30.3 Å / Num. obs: 5806 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.606 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.55
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 6.1 / Num. measured obs: 2232 / Num. unique obs: 648 / % possible all: 90.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.51
Highest resolutionLowest resolution
Rotation2.2 Å30.29 Å
Translation2.2 Å30.29 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U1T

1u1t


Resolution: 2.31→30.29 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.85 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.259 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.667 / SU B: 11.773 / SU ML: 0.275 / SU R Cruickshank DPI: 0.099 / SU Rfree: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.286 285 4.9 %RANDOM
Rwork0.272 ---
obs0.273 5805 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 42.01 Å2 / Biso mean: 18.63 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2--2.53 Å20 Å2
3----5.07 Å2
Refinement stepCycle: LAST / Resolution: 2.31→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 0 0 940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022954
X-RAY DIFFRACTIONr_angle_refined_deg2.5471.9691298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8535116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4352536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.71315174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.052156
X-RAY DIFFRACTIONr_chiral_restr0.1540.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021678
X-RAY DIFFRACTIONr_mcbond_it0.9841.5600
X-RAY DIFFRACTIONr_mcangle_it1.722980
X-RAY DIFFRACTIONr_scbond_it2.183354
X-RAY DIFFRACTIONr_scangle_it3.7614.5318
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A240TIGHT POSITIONAL0.170.05
B230MEDIUM POSITIONAL0.330.5
A240TIGHT THERMAL0.430.5
B230MEDIUM THERMAL0.522
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 10 -
Rwork0.429 390 -
all-400 -
obs--94.34 %

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