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- PDB-4noy: Crystal structure of Listeria monocytogenes Hfq F43W -

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Basic information

Entry
Database: PDB / ID: 4noy
TitleCrystal structure of Listeria monocytogenes Hfq F43W
ComponentsProtein Hfq
KeywordsRNA BINDING PROTEIN / LSm/Sm proteins / RNA chaperone
Function / homologySH3 type barrels. - #100 / SH3 type barrels. / Roll / Mainly Beta / S-1,2-PROPANEDIOL / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsCanty, J.T. / Kovach, 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 20, 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 / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,19314
Polymers52,5846
Non-polymers6098
Water54030
1
D: Protein Hfq
A: Protein Hfq
B: Protein Hfq
hetero molecules

D: Protein Hfq
A: Protein Hfq
B: Protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,49718
Polymers52,5846
Non-polymers91312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area12700 Å2
ΔGint7 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: Protein Hfq
E: Protein Hfq
F: Protein Hfq
hetero molecules

C: Protein Hfq
E: Protein Hfq
F: Protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88810
Polymers52,5846
Non-polymers3044
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area11180 Å2
ΔGint-31 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.957, 66.967, 106.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETASNASNchain AAB1 - 731 - 73
2LYSLYSLEULEUchain BBC2 - 722 - 72
3LYSLYSPROPROchain CCD2 - 742 - 74
4GLNGLNALAALAchain DDA3 - 713 - 71
5METMETLEULEUchain EEE1 - 721 - 72
6METMETASPASPchain FFF1 - 751 - 75

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Components

#1: Protein
Protein Hfq


Mass: 8763.989 Da / Num. of mol.: 6 / Mutation: F43W
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
#2: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.795→66.967 Å / Num. obs: 11574 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.25 Å2 / Rmerge(I) obs: 0.124 / Χ2: 2.13 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.795-2.853.70.3845241.135195.8
2.85-2.93.90.3635871.192198.2
2.9-2.964.30.3645451.246198.4
2.96-3.024.30.3315711.423199.3
3.02-3.084.30.2955701.582199.1
3.08-3.154.30.2645651.534198.6
3.15-3.234.20.2435721.943199.1
3.23-3.324.30.235781.892199.1
3.32-3.424.30.1755742.083199
3.42-3.534.20.1655782.024199
3.53-3.654.30.1515682.367199.5
3.65-3.84.30.1335892.424198.8
3.8-3.974.30.1385722.271199
3.97-4.184.20.0995762.67198.8
4.18-4.4440.0785802.746198.1
4.44-4.7940.0745842.764198.6
4.79-5.274.20.0815902.592198.8
5.27-6.034.20.1055982.509198.4
6.03-7.594.10.0926082.753199
7.59-503.70.0596453.224196.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NL2

4nl2


Resolution: 2.795→42.425 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7728 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML / Details: ATOM N PHE A 57 IS MODELED WITH B = 0.
RfactorNum. reflection% reflection
Rfree0.2847 548 4.75 %
Rwork0.2271 10977 -
obs0.2298 11525 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.91 Å2 / Biso mean: 19.2637 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.795→42.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 40 30 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143513
X-RAY DIFFRACTIONf_angle_d1.4644731
X-RAY DIFFRACTIONf_chiral_restr0.086538
X-RAY DIFFRACTIONf_plane_restr0.006605
X-RAY DIFFRACTIONf_dihedral_angle_d17.7471260
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2036X-RAY DIFFRACTION24.575TORSIONAL
12B2036X-RAY DIFFRACTION24.575TORSIONAL
13C2036X-RAY DIFFRACTION24.575TORSIONAL
14D2036X-RAY DIFFRACTION24.575TORSIONAL
15E2036X-RAY DIFFRACTION24.575TORSIONAL
16F2036X-RAY DIFFRACTION24.575TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7951-3.07630.32761270.25022593272094
3.0763-3.52130.29721270.23482752287999
3.5213-4.43570.28811490.20632757290699
4.4357-42.42960.25771450.23252875302098

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