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- PDB-4nl2: Crystal Structure of Listeria monocytogenes Hfq -

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Basic information

Entry
Database: PDB / ID: 4nl2
TitleCrystal Structure of Listeria monocytogenes Hfq
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 / molecular replacement / Resolution: 2.6 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)52,88213
Polymers52,3506
Non-polymers5337
Water70339
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)53,11116
Polymers52,3506
Non-polymers76110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area12040 Å2
ΔGint-14 kcal/mol
Surface area21070 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)52,65410
Polymers52,3506
Non-polymers3044
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11080 Å2
ΔGint-29 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 66.850, 106.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Protein hfq


Mass: 8724.953 Da / Num. of mol.: 6
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.: 7 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 43.12 %
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: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→106.51 Å / Num. all: 14557 / Num. obs: 14557 / % possible obs: 100 % / Redundancy: 5.8 % / Rsym value: 0.12 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.745.80.471.61205620630.47100
2.74-2.915.80.3562.11162419880.356100
2.91-3.115.90.2382.81078618400.238100
3.11-3.365.90.15351029917600.153100
3.36-3.685.90.1146.5938515960.114100
3.68-4.115.80.0967.4849914600.096100
4.11-4.755.80.0778.2759213080.077100
4.75-5.815.80.0788.3644411200.078100
5.81-8.225.60.087.950008900.08100
8.22-46.0785.10.0676.526905320.06799.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å46.08 Å
Translation2.6 Å46.08 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.5.1phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.078 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8069 / SU ML: 0.35 / σ(F): 1.38 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 730 5.03 %
Rwork0.2129 13792 -
obs0.2159 14522 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.26 Å2 / Biso mean: 40.9897 Å2 / Biso min: 20.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 35 39 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013596
X-RAY DIFFRACTIONf_angle_d1.4814823
X-RAY DIFFRACTIONf_chiral_restr0.091551
X-RAY DIFFRACTIONf_plane_restr0.008618
X-RAY DIFFRACTIONf_dihedral_angle_d15.0391325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6001-2.80080.30711340.242127142848
2.8008-3.08260.30981520.243726942846
3.0826-3.52850.28061630.21227222885
3.5285-4.4450.26331390.197227632902
4.445-46.08530.24311420.205628993041

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