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- PDB-2qtx: Crystal structure of an Hfq-like protein from Methanococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 2qtx
TitleCrystal structure of an Hfq-like protein from Methanococcus jannaschii
ComponentsUncharacterized protein MJ1435
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 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein MJ1435
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsNielsen, J.S. / Boggild, A. / Andersen, C.B.F. / Nielsen, G. / Boysen, A. / Brodersen, D.E. / Valentin-Hansen, P.
CitationJournal: Rna / Year: 2007
Title: An Hfq-like protein in archaea: Crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii.
Authors: Nielsen, J.S. / Boggild, A. / Andersen, C.B. / Nielsen, G. / Boysen, A. / Brodersen, D.E. / Valentin-Hansen, P.
History
DepositionAug 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uncharacterized protein MJ1435
B: Uncharacterized protein MJ1435
C: Uncharacterized protein MJ1435
D: Uncharacterized protein MJ1435
E: Uncharacterized protein MJ1435
F: Uncharacterized protein MJ1435
G: Uncharacterized protein MJ1435
H: Uncharacterized protein MJ1435
I: Uncharacterized protein MJ1435
J: Uncharacterized protein MJ1435
K: Uncharacterized protein MJ1435
L: Uncharacterized protein MJ1435


Theoretical massNumber of molelcules
Total (without water)99,71712
Polymers99,71712
Non-polymers00
Water2,342130
1
A: Uncharacterized protein MJ1435
B: Uncharacterized protein MJ1435
C: Uncharacterized protein MJ1435
D: Uncharacterized protein MJ1435
E: Uncharacterized protein MJ1435
F: Uncharacterized protein MJ1435


Theoretical massNumber of molelcules
Total (without water)49,8596
Polymers49,8596
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
MethodPISA
2
G: Uncharacterized protein MJ1435
H: Uncharacterized protein MJ1435
I: Uncharacterized protein MJ1435
J: Uncharacterized protein MJ1435
K: Uncharacterized protein MJ1435
L: Uncharacterized protein MJ1435


Theoretical massNumber of molelcules
Total (without water)49,8596
Polymers49,8596
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.866, 67.110, 119.064
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homohexamer. The asu contains two hexamers.

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Components

#1: Protein
Uncharacterized protein MJ1435


Mass: 8309.771 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pTYP11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 derivative (delta-hfq) / References: UniProt: Q58830
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 25% PEG 3350, 0.2M Ammonium Acetate, 0.1M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9993
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2006 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: FIXED EXIT SI 111 MONCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9993 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 17 / Number: 96326 / Rmerge(I) obs: 0.056 / Χ2: 1.5 / D res high: 2.5 Å / D res low: 250 Å / Num. obs: 28424 / % possible obs: 92.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.3925099.110.0291.7573.6
4.275.3999.910.0321.7233.8
3.734.2710010.0421.6883.8
3.393.7399.310.0581.5433.6
3.153.3976.510.0791.4242.2
2.963.1510.1251.339
2.822.9610.1661.349
2.692.8210.1851.196
2.592.6910.2381.188
2.52.5910.2091.152
ReflectionResolution: 2.5→250 Å / Num. obs: 28424 / % possible obs: 92.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.18 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.7 / % possible all: 57.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å38.5 Å
Translation2.5 Å38.5 Å
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.62 / Reflection: 28398 / Reflection acentric: 27025 / Reflection centric: 1373
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.2-38.5040.860.870.813641166198
4.5-7.20.840.850.741103796314
3.6-4.50.840.850.7151674867300
3.1-3.60.750.750.651844934250
2.7-3.10.460.460.3688458537308
2.5-2.70.210.210.08372837253

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.11phasing
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1S

1u1s


Resolution: 2.5→38.5 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1422 5.01 %RANDOM
Rwork0.18 ---
all-28393 --
obs-28393 92.2 %-
Solvent computationBsol: 30.003 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 41.43 Å2
Baniso -1Baniso -2Baniso -3
1-10.309 Å20 Å2-6.041 Å2
2---6.476 Å20 Å2
3----3.833 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5615 0 0 130 5745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_bond_d_na
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg0.928
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d14.5
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 54
RfactorNum. reflection% reflection
Rfree0.347 70 -
Rwork0.227 256 -
obs--0.56 %

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