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- PDB-4mml: D40A Hfq from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4mml
TitleD40A Hfq from Pseudomonas aeruginosa
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / LSM fold
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of carbon utilization / regulation of RNA stability / quorum sensing / regulation of translation / 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
URIDINE-5'-MONOPHOSPHATE / RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsMurina, V.N. / Filimonov, V.V. / Melnik, B.S. / Uhlein, M. / Mueller, U. / Weiss, M. / Nikulin, A.D.
CitationJournal: Biochemistry Mosc. / Year: 2014
Title: Effect of conserved intersubunit amino Acid substitutions on hfq protein structure and stability.
Authors: Murina, V.N. / Melnik, B.S. / Filimonov, V.V. / Uhlein, M. / Weiss, M.S. / Muller, U. / Nikulin, A.D.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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
A: Protein hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5154
Polymers9,0701
Non-polymers4453
Water45025
1
A: Protein hfq
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)57,09024
Polymers54,4236
Non-polymers2,66718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area11890 Å2
ΔGint-236 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.790, 65.790, 28.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-102-

MG

21A-213-

HOH

31A-215-

HOH

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Components

#1: Protein Protein hfq / bacterial translational regulator Hfq


Mass: 9070.478 Da / Num. of mol.: 1 / Mutation: D40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hfq, PA4944 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% w/v PEG2000 MME, 2% MPD, 20 micromolar zinc chloride, 50 mM Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2009
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. all: 6611 / Num. obs: 6611 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.1 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1418)refinement
PROCESSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1S
Resolution: 1.801→32.895 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2029 311 4.75 %
Rwork0.1638 --
obs0.1718 6611 98.54 %
all-6611 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 1.801→32.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms535 0 26 25 586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008570
X-RAY DIFFRACTIONf_angle_d1.09775
X-RAY DIFFRACTIONf_dihedral_angle_d13.677216
X-RAY DIFFRACTIONf_chiral_restr0.03994
X-RAY DIFFRACTIONf_plane_restr0.00493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8044-1.98540.24561520.25922929X-RAY DIFFRACTION93
1.9854-2.27130.21431350.20072940X-RAY DIFFRACTION94
2.2713-2.85620.24111560.18122947X-RAY DIFFRACTION94
2.8562-12.7080.18741420.1412974X-RAY DIFFRACTION95

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