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- PDB-4jli: Crystal Structure of Escherichia coli Hfq Proximal Pore Mutant -

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Basic information

Entry
Database: PDB / ID: 4jli
TitleCrystal Structure of Escherichia coli Hfq Proximal Pore Mutant
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / Riboregulator / Post-transcriptional regulator
Function / homologySH3 type barrels. - #100 / SH3 type barrels. / Roll / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRobinson, K.E. / Orans, J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching.
Authors: Robinson, K.E. / Orans, J. / Kovach, A.R. / Link, T.M. / Brennan, R.G.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein hfq
B: Protein hfq


Theoretical massNumber of molelcules
Total (without water)15,3482
Polymers15,3482
Non-polymers00
Water1,60389
1
A: Protein hfq
B: Protein hfq

A: Protein hfq
B: Protein hfq

A: Protein hfq
B: Protein hfq


Theoretical massNumber of molelcules
Total (without water)46,0436
Polymers46,0436
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9200 Å2
ΔGint-84 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.003, 104.003, 28.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-102-

HOH

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Components

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


Mass: 7673.911 Da / Num. of mol.: 2 / Fragment: UNP residues 2-69 / Mutation: F42W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hfq, O3O_02600 / References: UniProt: K0BDC5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.91 Å3/Da / Density % sol: 35.65 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.79→21.71 Å / Num. obs: 10698 / Rsym value: 0.059

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→21.71 Å / SU ML: 0.13 / σ(F): 2 / Phase error: 25.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2298 513 4.8 %
Rwork0.1796 --
obs0.182 10698 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 0 89 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051072
X-RAY DIFFRACTIONf_angle_d1.0311465
X-RAY DIFFRACTIONf_dihedral_angle_d15.55410
X-RAY DIFFRACTIONf_chiral_restr0.072176
X-RAY DIFFRACTIONf_plane_restr0.004185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7904-1.97050.26481250.21392556X-RAY DIFFRACTION100
1.9705-2.25540.28251280.20432533X-RAY DIFFRACTION100
2.2554-2.84060.27761250.20542560X-RAY DIFFRACTION100
2.8406-21.71150.19041350.15512536X-RAY DIFFRACTION100

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