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- PDB-5i21: Y55W Hfq from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5i21
TitleY55W Hfq from Pseudomonas aeruginosa
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / Hfq / Pseudomonas aeruginosa
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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNikulin, A.D. / Lekontseva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research14-04-31215 Russian Federation
CitationJournal: To Be Published
Title: Y55W Hfq from Pseudomonas aeruginosa
Authors: Nikulin, A.D. / Lekontseva, N.V.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4484
Polymers27,4133
Non-polymers351
Water3,567198
1
A: RNA-binding protein Hfq
C: RNA-binding protein Hfq
hetero molecules

A: RNA-binding protein Hfq
C: RNA-binding protein Hfq
hetero molecules

A: RNA-binding protein Hfq
C: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9329
Polymers54,8256
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9090 Å2
ΔGint-99 kcal/mol
Surface area18680 Å2
MethodPISA
2
B: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)54,8256
Polymers54,8256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area8920 Å2
ΔGint-73 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.362, 114.362, 28.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11C-105-

HOH

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Components

#1: Protein RNA-binding protein Hfq


Mass: 9137.524 Da / Num. of mol.: 3 / Mutation: Y55W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria)
Gene: hfq, PSPA7_5673 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6VD57
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% W/V PEG2000 MME, 2% MPD, 50 MM TRIS-HCL, PH 6.5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.86 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 31293 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 16.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04633 / Net I/σ(I): 25.89
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.5224 / Mean I/σ(I) obs: 4.09 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1S

1u1s


Resolution: 1.55→37.434 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 1528 4.88 %Random
Rwork0.1877 ---
obs0.1889 31284 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 1 198 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061624
X-RAY DIFFRACTIONf_angle_d0.8382209
X-RAY DIFFRACTIONf_dihedral_angle_d12.9121001
X-RAY DIFFRACTIONf_chiral_restr0.06267
X-RAY DIFFRACTIONf_plane_restr0.005274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.60010.24081560.21412625X-RAY DIFFRACTION99
1.6001-1.65730.20811580.20022690X-RAY DIFFRACTION100
1.6573-1.72370.23271210.20942640X-RAY DIFFRACTION100
1.7237-1.80210.23551570.20132682X-RAY DIFFRACTION100
1.8021-1.89710.21331440.18322687X-RAY DIFFRACTION100
1.8971-2.0160.24861120.19682709X-RAY DIFFRACTION100
2.016-2.17160.22581400.18722716X-RAY DIFFRACTION100
2.1716-2.39010.21491340.18052695X-RAY DIFFRACTION100
2.3901-2.73590.2041440.19922718X-RAY DIFFRACTION100
2.7359-3.44660.20931260.19022753X-RAY DIFFRACTION100
3.4466-37.44470.19951360.17162841X-RAY DIFFRACTION100

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