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- PDB-3inz: H57T Hfq from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3inz
TitleH57T Hfq from Pseudomonas aeruginosa
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / Hfq / protein tertiary structure / RNA-binding / Stress response / RNA-BINDING PROTEIN
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
: / RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoskaleva, O. / Melnik, B. / Gabdulkhakov, A. / Garber, M. / Nikonov, S. / Stolboushkina, E. / Nikulin, A.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The structures of mutant forms of Hfq from Pseudomonas aeruginosa reveal the importance of the conserved His57 for the protein hexamer organization.
Authors: Moskaleva, O. / Melnik, B. / Gabdulkhakov, A. / Garber, M. / Nikonov, S. / Stolboushkina, E. / Nikulin, A.
History
DepositionAug 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_keywords / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)55,53517
Polymers54,4656
Non-polymers1,07011
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-152 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.290, 71.160, 104.410
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: 9077.444 Da / Num. of mol.: 6 / Mutation: H57T
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
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 4 mg/ml protein, 50 mM NaCl, 100 mM NH4Cl, 7,5% MMEPEG 2000, 50 mM Tris HCl, 10 mM CdCl2, pH 8.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 50597 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.9
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2983 / % possible all: 80.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.4_4)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1S

1u1s


Resolution: 1.7→30 Å / SU ML: 0.03 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 2528 5 %RANDOM
Rwork0.1493 ---
obs0.1527 50571 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.003 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 1.1587 Å2
Baniso -1Baniso -2Baniso -3
1-10.0037 Å20.1308 Å2-10.3297 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 11 379 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013392
X-RAY DIFFRACTIONf_angle_d1.3154626
X-RAY DIFFRACTIONf_dihedral_angle_d14.5961302
X-RAY DIFFRACTIONf_chiral_restr0.103564
X-RAY DIFFRACTIONf_plane_restr0.006582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6982-1.73080.2471310.17822475X-RAY DIFFRACTION93
1.7308-1.76610.27921350.17442583X-RAY DIFFRACTION98
1.7661-1.80450.30741390.19312644X-RAY DIFFRACTION98
1.8045-1.84650.29341360.19512591X-RAY DIFFRACTION98
1.8465-1.89270.26451390.16442642X-RAY DIFFRACTION99
1.8927-1.94380.21311400.12552651X-RAY DIFFRACTION100
1.9438-2.0010.20241410.12532669X-RAY DIFFRACTION100
2.001-2.06560.21661410.12352676X-RAY DIFFRACTION100
2.0656-2.13940.21611400.13572674X-RAY DIFFRACTION100
2.1394-2.2250.21491420.12962697X-RAY DIFFRACTION100
2.225-2.32620.2551400.13772663X-RAY DIFFRACTION100
2.3262-2.44880.2141420.13692691X-RAY DIFFRACTION100
2.4488-2.60210.28421420.14682704X-RAY DIFFRACTION100
2.6021-2.80290.21471430.15832701X-RAY DIFFRACTION100
2.8029-3.08460.2351430.15192726X-RAY DIFFRACTION100
3.0846-3.53030.21741440.15092725X-RAY DIFFRACTION100
3.5303-4.44490.17651450.13212768X-RAY DIFFRACTION100
4.4449-28.14980.17091450.14742763X-RAY DIFFRACTION95

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