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- PDB-4ht8: Crystal structure of E coli Hfq bound to poly(A) A7 -

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Basic information

Entry
Database: PDB / ID: 4ht8
TitleCrystal structure of E coli Hfq bound to poly(A) A7
Components
  • Protein hfq
  • RNA (5'-R(*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / Hfq / poly(A) / Sm Fold / RNA chaperone / single stranded RNA / cytoplasmic / RNA BINDING PROTEIN-RNA 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
RNA / RNA-binding protein Hfq / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWang, W.W. / Wang, L.J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA.
Authors: Wang, W. / Wang, L. / Wu, J. / Gong, Q. / Shi, Y.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
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
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: Protein hfq
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq
I: RNA (5'-R(*AP*AP*AP*AP*AP*AP*A)-3')
K: RNA (5'-R(*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)48,4728
Polymers48,4728
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-61 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.990, 40.710, 100.850
Angle α, β, γ (deg.)90.000, 101.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein hfq / HF-1 / Host factor-I protein


Mass: 7325.554 Da / Num. of mol.: 6 / Fragment: Sm fold
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / BL21-DE3 / Gene: B21_04001, ECBD_3862, ECD_04039, hfq / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6ECV6, UniProt: A0A140NGK1*PLUS
#2: RNA chain RNA (5'-R(*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2259.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 200 mM NH4Ac, 100 Tris, 26% 2-propanol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→98.874 Å / Num. all: 45603 / Num. obs: 45603 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.70.2143.52439266440.214100
1.79-1.93.70.1415.22307762970.141100
1.9-2.033.60.1056.22162059420.105100
2.03-2.193.60.0817.71996555130.08199.9
2.19-2.43.60.06991835751110.06999.9
2.4-2.693.60.058101665146110.05899.9
2.69-3.13.70.0737.61521641230.073100
3.1-3.83.70.0639.31290334510.063100
3.8-5.383.60.04313.8936026240.04396.6
5.38-31.153.40.03715.3431212870.03783.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å31.15 Å
Translation1.7 Å31.15 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 1.9→98.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2732 / WRfactor Rwork: 0.2141 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8644 / SU B: 6.709 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1575 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 6.2 / ESU R: 0.158 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 1651 5 %RANDOM
Rwork0.1895 ---
all0.269 33093 --
obs0.1917 32695 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.7 Å2 / Biso mean: 33.147 Å2 / Biso min: 2.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20.12 Å2
2--0.13 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→98.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 282 0 180 3226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223197
X-RAY DIFFRACTIONr_angle_refined_deg1.3452.0864422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06225.229109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4215484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.763158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212250
X-RAY DIFFRACTIONr_mcbond_it0.6111.51855
X-RAY DIFFRACTIONr_mcangle_it1.07523029
X-RAY DIFFRACTIONr_scbond_it1.65131342
X-RAY DIFFRACTIONr_scangle_it2.5874.51388
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 141 -
Rwork0.192 2294 -
all-2435 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9926-0.5664-1.46182.16491.05263.3403-0.0052-0.06880.05130.2721-0.0006-0.1316-0.04020.14350.00580.19990.008-0.03810.00930.00460.08821.29484.381241.8959
24.2389-0.93820.08241.8210.30684.0071-0.0234-0.0209-0.03930.2459-0.13460.2694-0.1363-0.51530.1580.12920.04120.05280.0923-0.03880.12153.96913.111236.8556
34.1093-2.02390.80362.8460.91076.29620.00510.4599-0.27580.1026-0.40540.5071-0.0084-0.8170.40030.01970.0353-0.00780.2988-0.14140.1679-0.6664-0.019919.3321
45.0102-0.6853-2.59533.27360.68765.1210.07051.09-0.128-0.3148-0.23290.2013-0.0909-0.53840.16240.06980.0897-0.05520.3937-0.07240.05612.3586-3.10566.8276
54.7186-0.0002-0.62711.74570.38524.19830.09910.5320.027-0.0859-0.021-0.1408-0.13530.3993-0.0780.05030.0570.02170.2028-0.00130.059529.5797-2.640511.4396
62.51430.26830.20493.03821.44566.1694-0.01820.04860.05380.10180.2251-0.5384-0.09360.8502-0.20690.05250.0102-0.03610.1306-0.02870.163334.5011.347928.923
73.4352-0.7766-2.74810.96030.4434.7532-0.15530.1417-0.46950.2364-0.08240.03490.54240.12970.23770.29220.0584-0.02860.0443-0.01490.261825.2277-12.051133.7127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 65
2X-RAY DIFFRACTION2B6 - 65
3X-RAY DIFFRACTION3C6 - 65
4X-RAY DIFFRACTION4D5 - 65
5X-RAY DIFFRACTION5E6 - 65
6X-RAY DIFFRACTION6F6 - 65
7X-RAY DIFFRACTION7I1 - 7

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