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- PDB-3qui: Crystal structure of Pseudomonas aeruginosa Hfq in complex with ADPNP -

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Basic information

Entry
Database: PDB / ID: 3qui
TitleCrystal structure of Pseudomonas aeruginosa Hfq in complex with ADPNP
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / LSM / RNA-binding protein / sRNA / mRNA / RNA CHAPERONE
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
ADENINE / ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.933 Å
AuthorsNikulin, A.D. / Murina, V.N. / Gabdulkhakov, A.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Hfq binds ribonucleotides in three different RNA-binding sites.
Authors: Murina, V. / Lekontseva, N. / Nikulin, A.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 13, 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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,72814
Polymers54,6876
Non-polymers3,0418
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-77 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.083, 75.862, 93.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Protein hfq


Mass: 9114.487 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hfq, PA4944 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0

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Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200 mM ammonium sulphate, 200 mM NaCl, 50 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Oct 9, 2010
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 29725 / Num. obs: 29725 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→2.04 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.97 / Num. unique all: 3127 / % possible all: 66.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1T

1u1t


Resolution: 1.933→47.577 Å / SU ML: 0.25 / Isotropic thermal model: OVERALL ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2872 1519 5.12 %RANDOM 5%
Rwork0.2129 ---
all0.2296 29670 --
obs0.2168 29670 89.32 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.774 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.9315 Å2-0 Å20 Å2
2---6.4423 Å20 Å2
3---17.3739 Å2
Refinement stepCycle: LAST / Resolution: 1.933→47.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 191 210 3656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073554
X-RAY DIFFRACTIONf_angle_d1.1164862
X-RAY DIFFRACTIONf_dihedral_angle_d16.5111372
X-RAY DIFFRACTIONf_chiral_restr0.074568
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9328-1.99520.3347820.29291720X-RAY DIFFRACTION60
1.9952-2.06660.35641180.28512096X-RAY DIFFRACTION74
2.0666-2.14930.3408910.26012243X-RAY DIFFRACTION79
2.1493-2.24710.33831280.242387X-RAY DIFFRACTION85
2.2471-2.36560.28881500.23122541X-RAY DIFFRACTION90
2.3656-2.51380.32711620.23352700X-RAY DIFFRACTION96
2.5138-2.70790.32361360.23612832X-RAY DIFFRACTION99
2.7079-2.98030.33231480.23172846X-RAY DIFFRACTION100
2.9803-3.41150.28991640.20172879X-RAY DIFFRACTION100
3.4115-4.29770.26271690.17712893X-RAY DIFFRACTION100
4.2977-47.59160.23341710.18433014X-RAY DIFFRACTION99

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