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- PDB-6xyj: Hfq from E.coli with inserted long loop L4 sequence -

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Basic information

Entry
Database: PDB / ID: 6xyj
TitleHfq from E.coli with inserted long loop L4 sequence
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / Hfq / SmAP / tertiary structure / RNA-chaperon
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 / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.772 Å
AuthorsNikulin, A.D. / Alipov, A.A. / Lekontseva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00222 Russian Federation
CitationJournal: Crystallography Reports / Year: 2021
Title: Structure of a Mutant Form of Translation Regulator Hfq with the Extended Loop L4
Authors: Alipov, A.A. / Lekontseva, N.V. / Mikhailina, A.O. / Fando, M.S. / Tishchenko, S.V. / Nikulin, A.D.
History
DepositionJan 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: RNA-binding protein Hfq
BBB: RNA-binding protein Hfq
CCC: RNA-binding protein Hfq
DDD: RNA-binding protein Hfq
EEE: RNA-binding protein Hfq
FFF: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)63,4156
Polymers63,4156
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-65 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.811, 112.616, 78.054
Angle α, β, γ (deg.)90.000, 119.434, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
RNA-binding protein Hfq


Mass: 10569.116 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria)
Strain: PA7 / Gene: hfq, PSPA7_5673 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6VD57
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% PEG 400, 50 mM PIPES 7.0, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 14459 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.069 / Rrim(I) all: 0.1 / Χ2: 0.52 / Net I/σ(I): 6.9
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.269 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1895 / CC1/2: 0.584 / Rpim(I) all: 1.134 / Rrim(I) all: 1.611 / Χ2: 0.5 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1S

1u1s


Resolution: 2.772→43.401 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.904 / SU B: 28.317 / SU ML: 0.515 / Cross valid method: FREE R-VALUE / ESU R Free: 0.428
RfactorNum. reflection% reflection
Rfree0.2846 715 4.945 %
Rwork0.211 --
all0.215 --
obs-14458 98.1 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 97.738 Å2
Baniso -1Baniso -2Baniso -3
1--1.443 Å2-0 Å25.328 Å2
2---7.485 Å20 Å2
3---1.781 Å2
Refinement stepCycle: LAST / Resolution: 2.772→43.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 0 1 3862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133926
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173868
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6445323
X-RAY DIFFRACTIONr_angle_other_deg1.1311.5728976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44622.069203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65715735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841530
X-RAY DIFFRACTIONr_chiral_restr0.0570.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024237
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02749
X-RAY DIFFRACTIONr_nbd_refined0.2240.2735
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.23970
X-RAY DIFFRACTIONr_nbtor_refined0.160.21804
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1810.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.225
X-RAY DIFFRACTIONr_nbd_other0.2310.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.22
X-RAY DIFFRACTIONr_mcbond_it6.13410.1691918
X-RAY DIFFRACTIONr_mcbond_other6.13110.1671917
X-RAY DIFFRACTIONr_mcangle_it9.04415.242387
X-RAY DIFFRACTIONr_mcangle_other9.04315.2442388
X-RAY DIFFRACTIONr_scbond_it6.20710.8582007
X-RAY DIFFRACTIONr_scbond_other6.20510.8612008
X-RAY DIFFRACTIONr_scangle_it9.54616.0352934
X-RAY DIFFRACTIONr_scangle_other9.54516.0382935
X-RAY DIFFRACTIONr_lrange_it12.861116.9114074
X-RAY DIFFRACTIONr_lrange_other12.861116.9384075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.772-2.8440.474390.412852X-RAY DIFFRACTION80.6335
2.844-2.9220.388640.368974X-RAY DIFFRACTION99.6161
2.922-3.0060.322610.321953X-RAY DIFFRACTION99.6071
3.006-3.0990.346490.308954X-RAY DIFFRACTION100
3.099-3.20.324540.26890X-RAY DIFFRACTION99.6832
3.2-3.3120.328260.261907X-RAY DIFFRACTION99.8929
3.312-3.4370.225330.214876X-RAY DIFFRACTION99.5619
3.437-3.5770.245480.199829X-RAY DIFFRACTION99.7725
3.577-3.7350.301370.19783X-RAY DIFFRACTION99.3939
3.735-3.9170.316350.215769X-RAY DIFFRACTION99.382
3.917-4.1280.3360.196709X-RAY DIFFRACTION99.466
4.128-4.3780.224370.174684X-RAY DIFFRACTION100
4.378-4.6780.224300.139649X-RAY DIFFRACTION99.269
4.678-5.0510.227210.169600X-RAY DIFFRACTION99.36
5.051-5.530.375310.215554X-RAY DIFFRACTION99.1525
5.53-6.1780.406160.206509X-RAY DIFFRACTION99.2439
6.178-7.1240.383320.225432X-RAY DIFFRACTION99.5708
7.124-8.7010.231270.17372X-RAY DIFFRACTION99.5012
8.701-12.2060.212220.155277X-RAY DIFFRACTION98.3553
12.206-43.40.289170.264170X-RAY DIFFRACTION97.3958

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