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- PDB-5dy9: Y68T Hfq from Methanococcus jannaschii in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 5dy9
TitleY68T Hfq from Methanococcus jannaschii in complex with AMP
ComponentsHfq-like protein
KeywordsRNA BINDING PROTEIN / Hfq / Lsm protein / ribonucleotide-protein complex
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
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / Uncharacterized protein MJ1435
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNikulin, A.D. / Mikhailina, A.O. / Lekontseva, N.V. / Balobanov, V.A. / Nikonova, E.Y. / Tishchenko, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Scientific Foundation14-14-00496 Russian Federation
CitationJournal: J. Biomol. Struct. Dyn. / Year: 2017
Title: Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii.
Authors: Nikulin, A. / Mikhailina, A. / Lekontseva, N. / Balobanov, V. / Nikonova, E. / Tishchenko, S.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hfq-like protein
B: Hfq-like protein
C: Hfq-like protein
D: Hfq-like protein
E: Hfq-like protein
F: Hfq-like protein
G: Hfq-like protein
H: Hfq-like protein
I: Hfq-like protein
J: Hfq-like protein
K: Hfq-like protein
L: Hfq-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,58335
Polymers98,97212
Non-polymers2,61023
Water18,6641036
1
A: Hfq-like protein
B: Hfq-like protein
C: Hfq-like protein
D: Hfq-like protein
E: Hfq-like protein
F: Hfq-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,92617
Polymers49,4866
Non-polymers1,43911
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-107 kcal/mol
Surface area16910 Å2
MethodPISA
2
G: Hfq-like protein
H: Hfq-like protein
I: Hfq-like protein
J: Hfq-like protein
K: Hfq-like protein
L: Hfq-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,65718
Polymers49,4866
Non-polymers1,17112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-83 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.636, 67.635, 91.165
Angle α, β, γ (deg.)90.00, 90.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Hfq-like protein / Uncharacterized protein MJ1435


Mass: 8247.700 Da / Num. of mol.: 12 / Mutation: Y68T
Source method: isolated from a genetically manipulated source
Details: Y68T substitution
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: MJ1435 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58830

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Non-polymers , 8 types, 1059 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1036 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.87 % / Description: stick-shaped crystals
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50% PEG200, 100 mM Tris-HCl, pH 8.0 (JBScreen Nuc-Pro 1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 96577 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rsym value: 0.051 / Net I/σ(I): 18.17
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.28 / % possible all: 98

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 2100 2.17 %
Rwork0.169 --
obs0.1697 96568 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5611 0 159 1036 6806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075956
X-RAY DIFFRACTIONf_angle_d1.0718026
X-RAY DIFFRACTIONf_dihedral_angle_d13.4522279
X-RAY DIFFRACTIONf_chiral_restr0.046887
X-RAY DIFFRACTIONf_plane_restr0.0041014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63630.32111360.26736110X-RAY DIFFRACTION97
1.6363-1.67730.25341380.23316211X-RAY DIFFRACTION99
1.6773-1.72260.26471390.21646263X-RAY DIFFRACTION99
1.7226-1.77330.22111390.19956258X-RAY DIFFRACTION99
1.7733-1.83050.27771390.19136235X-RAY DIFFRACTION99
1.8305-1.8960.22541400.18896296X-RAY DIFFRACTION99
1.896-1.97190.21681390.17416274X-RAY DIFFRACTION99
1.9719-2.06160.21031390.17336277X-RAY DIFFRACTION99
2.0616-2.17030.21021410.16896325X-RAY DIFFRACTION100
2.1703-2.30630.18271390.15526265X-RAY DIFFRACTION100
2.3063-2.48430.20451410.17216345X-RAY DIFFRACTION100
2.4843-2.73430.20731420.17936357X-RAY DIFFRACTION100
2.7343-3.12990.21851410.16866373X-RAY DIFFRACTION100
3.1299-3.9430.1641420.14996399X-RAY DIFFRACTION100
3.943-500.17741450.15186480X-RAY DIFFRACTION100

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