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- PDB-4j5y: Crystal structure of Hfq from Pseudomonas aeruginosa in complex w... -

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Basic information

Entry
Database: PDB / ID: 4j5y
TitleCrystal structure of Hfq from Pseudomonas aeruginosa in complex with ATP
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / LSM / RNA chaperone / sRNA / mRNA
Function / homology
Function and homology information


regulation of carbon utilization / regulation of translation, ncRNA-mediated / 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
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.0953 Å
AuthorsMurina, V. / Lekontseva, N. / Nikulin, A.
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 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,37514
Polymers54,6876
Non-polymers2,6888
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-86 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.450, 73.680, 107.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hfq, PA4944 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 22, 2012 / Details: helios
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.095→20 Å / Num. all: 28097 / Num. obs: 28097 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.02
Reflection shellResolution: 2.095→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.33 / Num. unique all: 3877 / % possible all: 88.44

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1T

1u1t


Resolution: 2.0953→19.574 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1428 5.08 %random, 5%
Rwork0.1841 ---
all0.1876 28097 --
obs0.1876 28097 95.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0953→19.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 164 285 3730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073551
X-RAY DIFFRACTIONf_angle_d1.2944861
X-RAY DIFFRACTIONf_dihedral_angle_d15.5961366
X-RAY DIFFRACTIONf_chiral_restr0.078566
X-RAY DIFFRACTIONf_plane_restr0.006577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0953-2.17010.32381190.25522436X-RAY DIFFRACTION88
2.1701-2.25680.28621520.22192664X-RAY DIFFRACTION98
2.2568-2.35940.27071520.20822669X-RAY DIFFRACTION97
2.3594-2.48360.26841450.1962686X-RAY DIFFRACTION97
2.4836-2.63880.27841370.20812688X-RAY DIFFRACTION97
2.6388-2.8420.2851520.20192676X-RAY DIFFRACTION97
2.842-3.1270.27681370.19432695X-RAY DIFFRACTION97
3.127-3.5770.25061640.17012690X-RAY DIFFRACTION96
3.577-4.49770.21531330.15482704X-RAY DIFFRACTION95
4.4977-19.57510.20881370.15952761X-RAY DIFFRACTION93

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