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- PDB-2ylc: Structure of Salmonella typhimurium Hfq in complex with U6 RNA -

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Basic information

Entry
Database: PDB / ID: 2ylc
TitleStructure of Salmonella typhimurium Hfq in complex with U6 RNA
ComponentsPROTEIN HFQ
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / LSM PROTEIN / RNA CHAPERONE
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / RNA binding / identical protein 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
THIOCYANATE ION / URIDINE-5'-MONOPHOSPHATE / RNA-binding protein Hfq
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSauer, E. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural Basis for RNA 3' End Recognition by Hfq
Authors: Sauer, E. / Weichenrieder, O.
History
DepositionJun 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN HFQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6984
Polymers8,2581
Non-polymers4403
Water90150
1
A: PROTEIN HFQ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)52,18824
Polymers49,5456
Non-polymers2,64218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555y,-x+y,z1
Buried area11160 Å2
ΔGint-118.1 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.190, 61.190, 28.350
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 PROTEIN HFQ / HOST FACTOR-I PROTEIN / HF-I / HFQ PROTEIN


Mass: 8257.572 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-72
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE IS PRECEDED BY A GA TAG REMAINING FROM THE PURIFICATION TAG.
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: LT2 / Plasmid: PET M60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: P0A1R0
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS PRECEDED BY A GA TAG REMAINING FROM THE PURIFICATION TAG

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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: 40 % / Description: NONE
Crystal growpH: 8 / Details: 0.2 M NASCN, 20% PEG3350, pH 8.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→30.6 Å / Num. obs: 15112 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 13.31 Å2 / Rsym value: 0.077 / Net I/σ(I): 16.6
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YLB

2ylb


Resolution: 1.3→30.595 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 18.33 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. B FACTORS WERE REFINED ANISOTROPICALLY FOR NON-HYDROGEN ATOMS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUE ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. B FACTORS WERE REFINED ANISOTROPICALLY FOR NON-HYDROGEN ATOMS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUE 27. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1 TO 4, 71 TO 72. THE DENSITY FOR THE HEXAURIDINE RNA IS AVERAGED AROUND THE SIXFOLD AXIS. THE ASYMMETRIC UNIT CONTAINS ONLY ONE OF THE SIX URIDINES WITH A PHOSPHATE OCCUPANCY OF 5 OUT OF 6, AND WITH COVALENT BONDS TO ITS NUCLEOTIDE NEIGHBORS. THE BIOLOGICAL UNIT IS AN HFQ HEXAMER BOUND TO THE HEXAURIDINE RNA SUBSTRATE.
RfactorNum. reflection% reflection
Rfree0.1816 762 5 %
Rwork0.1317 --
obs0.1342 15112 99.93 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.967 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.6328 Å20 Å20 Å2
2---0.6328 Å20 Å2
3---1.2656 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 26 50 605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013570
X-RAY DIFFRACTIONf_angle_d1.5774
X-RAY DIFFRACTIONf_dihedral_angle_d14.853216
X-RAY DIFFRACTIONf_chiral_restr0.08894
X-RAY DIFFRACTIONf_plane_restr0.0195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.40050.2291390.1732854X-RAY DIFFRACTION100
1.4005-1.54140.20251490.14272847X-RAY DIFFRACTION100
1.5414-1.76450.17121640.11942857X-RAY DIFFRACTION100
1.7645-2.2230.17231560.10032845X-RAY DIFFRACTION100
2.223-30.60350.17981540.14072947X-RAY DIFFRACTION100

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