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- PDB-4nl3: Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA -

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Basic information

Entry
Database: PDB / ID: 4nl3
TitleCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA
Components
  • 5'-R(*UP*UP*UP*UP*UP*U)-3'
  • Protein hfq
KeywordsRNA BINDING PROTEIN/RNA / LSm/Sm proteins / RNA chaperone / sRNA / 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 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / : / RNA-binding protein Hfq
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKovach, A.R. / Brennan, R.G.
CitationJournal: Rna / Year: 2014
Title: Recognition of U-rich RNA by Hfq from the Gram-positive pathogen Listeria monocytogenes.
Authors: Kovach, A.R. / Hoff, K.E. / Canty, J.T. / Orans, J. / Brennan, R.G.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Item: _audit_author.name / _software.classification ..._audit_author.name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Protein hfq
A: Protein hfq
B: Protein hfq
C: Protein hfq
E: Protein hfq
F: Protein hfq
J: Protein hfq
G: Protein hfq
H: Protein hfq
I: Protein hfq
K: Protein hfq
L: Protein hfq
R: 5'-R(*UP*UP*UP*UP*UP*U)-3'
Z: 5'-R(*UP*UP*UP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)108,28414
Polymers108,28414
Non-polymers00
Water362
1
D: Protein hfq
A: Protein hfq
B: Protein hfq
J: Protein hfq
G: Protein hfq
H: Protein hfq
R: 5'-R(*UP*UP*UP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)54,1427
Polymers54,1427
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-119 kcal/mol
Surface area19100 Å2
MethodPISA
2
C: Protein hfq
E: Protein hfq
F: Protein hfq
I: Protein hfq
K: Protein hfq
L: Protein hfq
Z: 5'-R(*UP*UP*UP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)54,1427
Polymers54,1427
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-89 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.028, 123.934, 67.595
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L
12chain R
22chain Z

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASNASNchain AAB2 - 732 - 73
21LYSLYSLEULEUchain BBC2 - 722 - 72
31METMETPROPROchain CCD1 - 741 - 74
41METMETASNASNchain DDA1 - 731 - 73
51LYSLYSASNASNchain EEE2 - 732 - 73
61METMETASPASPchain FFF1 - 751 - 75
71METMETASNASNchain GGH1 - 731 - 73
81LYSLYSLEULEUchain HHI2 - 722 - 72
91METMETPROPROchain IIJ1 - 741 - 74
101METMETASNASNchain JJG1 - 731 - 73
111METMETASNASNchain KKK1 - 731 - 73
121METMETPROPROchain LLL1 - 741 - 74
12UUUUchain RRM17 - 221 - 6
22UUUUchain ZZN27 - 321 - 6

NCS ensembles :
ID
1
2

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Components

#1: Protein
Protein hfq


Mass: 8724.953 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: hfq, LMHCC_1277 / Production host: Escherichia coli (E. coli) / References: UniProt: B8DG33, UniProt: Q92C58*PLUS
#2: RNA chain 5'-R(*UP*UP*UP*UP*UP*U)-3'


Mass: 1792.037 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% 1,2-propanediol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2013
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 17828 / % possible obs: 95.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 53.28 Å2 / Rmerge(I) obs: 0.114 / Χ2: 1.666 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.152.10.3036391.114170.5
3.15-3.212.30.2637491.346179
3.21-3.272.50.2697961.049187
3.27-3.342.70.2478631.258192.6
3.34-3.4130.2298551.373195.5
3.41-3.493.20.2048951.328197
3.49-3.583.30.2119441.549199.4
3.58-3.683.40.2099241.666199.5
3.68-3.783.60.179031.643199.9
3.78-3.913.60.1839461.4561100
3.91-4.043.70.1529031.526199.8
4.04-4.213.70.1149341.6131100
4.21-4.43.60.0959451.9621100
4.4-4.633.60.0869221.908199.9
4.63-4.923.60.0949202.038199.9
4.92-5.33.60.0989421.831199.8
5.3-5.833.60.1139451.888199.8
5.83-6.673.60.0989132.011199.8
6.67-8.43.50.0739461.794199.8
8.4-503.30.0419441.791198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NL2

4nl2


Resolution: 3.1→45.675 Å / FOM work R set: 0.7677 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 29.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 907 5.11 %
Rwork0.2211 16853 -
obs0.2242 17760 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.01 Å2 / Biso mean: 36.02 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 234 0 2 7168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017292
X-RAY DIFFRACTIONf_angle_d1.1829859
X-RAY DIFFRACTIONf_chiral_restr0.0691137
X-RAY DIFFRACTIONf_plane_restr0.0051236
X-RAY DIFFRACTIONf_dihedral_angle_d16.6062733
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4242X-RAY DIFFRACTION20.533TORSIONAL
12B4242X-RAY DIFFRACTION20.533TORSIONAL
13C4242X-RAY DIFFRACTION20.533TORSIONAL
14D4242X-RAY DIFFRACTION20.533TORSIONAL
15E4242X-RAY DIFFRACTION20.533TORSIONAL
16F4242X-RAY DIFFRACTION20.533TORSIONAL
17G4242X-RAY DIFFRACTION20.533TORSIONAL
18H4242X-RAY DIFFRACTION20.533TORSIONAL
19I4242X-RAY DIFFRACTION20.533TORSIONAL
110J4242X-RAY DIFFRACTION20.533TORSIONAL
111K4242X-RAY DIFFRACTION20.533TORSIONAL
112L4242X-RAY DIFFRACTION20.533TORSIONAL
21R136X-RAY DIFFRACTION20.533TORSIONAL
22Z136X-RAY DIFFRACTION20.533TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0997-3.29380.3711240.25272319244380
3.2938-3.54810.34411570.24842838299596
3.5481-3.9050.30461500.232229103060100
3.905-4.46960.2541520.204529453097100
4.4696-5.62960.25931610.202129273088100
5.6296-45.67950.25481630.22232914307798

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