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- PDB-4y91: Crystal Structure of a Thermotoga maritima Hfq homolog -

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Basic information

Entry
Database: PDB / ID: 4y91
TitleCrystal Structure of a Thermotoga maritima Hfq homolog
Components
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
  • RNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN/RNA / Hfq / Sm protein / beta barrel / hexamer / RNA BINDING PROTEIN-RNA Complex
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 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / RNA-binding protein Hfq
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.656 Å
Model detailsFull N-terminal region could be built for chain I only; weak electron density for residues 1-7 in ...Full N-terminal region could be built for chain I only; weak electron density for residues 1-7 in this region, as well as some Ramachandran outliers and low-scoring rotamer states.
AuthorsRandolph, P.S. / Patterson, J. / Mura, C.
CitationJournal: To be published
Title: Crystal Structure of a Thermotoga maritima Hfq homolog
Authors: Patterson, J. / Randolph, P.S. / Mura, C.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_oper_list ...exptl_crystal_grow / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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
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
N: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
O: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)133,30714
Polymers133,30714
Non-polymers00
Water23413
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
O: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)66,6547
Polymers66,6547
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-84 kcal/mol
Surface area18440 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
N: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)66,6547
Polymers66,6547
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-81 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.080, 133.500, 206.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RNA-binding protein Hfq


Mass: 10810.246 Da / Num. of mol.: 12 / Fragment: Tma Hfq
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: hfq, TM_0526 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYZ6
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: tri-potassium citrate, PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97879 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2012 / Details: 300mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionNumber: 469281 / Rmerge(I) obs: 0.139 / Χ2: 0.99 / D res high: 2.65 Å / Num. obs: 32352 / % possible obs: 99.8
Diffraction reflection shellHighest resolution: 2.65 Å / Lowest resolution: 2.81 Å / Num. obs: 5090 / Rmerge(I) obs: 1.322
ReflectionResolution: 2.656→56.03 Å / Num. obs: 27360 / % possible obs: 84.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.56 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.123 / Χ2: 1.006 / Net I/σ(I): 25.39 / Num. measured all: 393986
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.66-2.720.9450.6165.85801723536410.64327.2
2.72-2.80.9730.5956.914169230210150.61844.1
2.8-2.880.9820.6047.0319080218513240.62660.6
2.88-2.970.990.5348.0222546218615430.55470.6
2.97-3.070.9910.5158.725853209817520.53483.5
3.07-3.170.9950.41410.3228384201819140.42994.8
3.17-3.290.9950.39110.7629258198019800.405100
3.29-3.430.9980.24515.8527831188318830.253100
3.43-3.580.9980.20118.2327116183918390.208100
3.58-3.760.9990.12624.4525285171917190.131100
3.76-3.960.9990.13624.0724881169916990.141100
3.96-4.20.9990.08932.1922818155715570.092100
4.2-4.490.9990.06839.8621586149314930.071100
4.49-4.8510.05247.2720405141514130.05499.9
4.85-5.3110.05446.4418193127412730.05699.9
5.31-5.940.9990.06243.0816853118411850.065100
5.94-6.860.9990.05645.0214708105110510.058100
6.86-8.410.04453.34124649089080.045100
8.4-11.880.9990.03167.8395987337330.032100
11.8810.02962.9749414414380.0399.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HSB

3hsb


Resolution: 2.656→56.03 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1372 5.02 %
Rwork0.1836 25978 -
obs0.1868 27350 84.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.79 Å2 / Biso mean: 29.9278 Å2 / Biso min: 6.52 Å2
Refinement stepCycle: final / Resolution: 2.656→56.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 240 0 13 6777
Biso mean---25.64 -
Num. residues----809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126909
X-RAY DIFFRACTIONf_angle_d1.4799365
X-RAY DIFFRACTIONf_chiral_restr0.0811094
X-RAY DIFFRACTIONf_plane_restr0.0061125
X-RAY DIFFRACTIONf_dihedral_angle_d16.8782577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6558-2.75070.2982550.224589494930
2.7507-2.86080.3214770.23211632170954
2.8608-2.9910.25621180.22142133225171
2.991-3.14870.30031460.2222671281789
3.1487-3.3460.34361550.217130403195100
3.346-3.60430.25321520.186530733225100
3.6043-3.96690.24691490.177830703219100
3.9669-4.54070.19811740.15130433217100
4.5407-5.71990.21321740.151431273301100
5.7199-56.04270.22571720.186232953467100

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