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- PDB-3m4g: H57A HFQ from Pseudomonas Aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3m4g
TitleH57A HFQ from Pseudomonas Aeruginosa
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / HFQ / protein tertiary structure / RNA-binding / protein stability / Stress response
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
RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMoskaleva, O. / Melnik, B. / Gabdulkhakov, A. / Garber, M. / Nikonov, S. / Stolboushkina, E. / Nikulin, A.
CitationJournal: 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
DepositionMar 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_conn.ptnr2_label_seq_id / _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

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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
G: Protein hfq
H: Protein hfq
I: Protein hfq
J: Protein hfq
K: Protein hfq
L: Protein hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,48526
Polymers108,56912
Non-polymers91614
Water6,035335
1
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)54,80814
Polymers54,2856
Non-polymers5238
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-336 kcal/mol
Surface area19150 Å2
MethodPISA
2
G: Protein hfq
H: Protein hfq
I: Protein hfq
J: Protein hfq
K: Protein hfq
L: Protein hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,67712
Polymers54,2856
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-275 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.460, 66.587, 68.713
Angle α, β, γ (deg.)91.78, 115.32, 119.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein hfq


Mass: 9047.418 Da / Num. of mol.: 12 / Mutation: H57A
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 4 MG/ML PROTEIN, 50 MM NACL, 100 MM NH4CL, 7,5% MMEPEG 2000, 50 MM TRIS HCL, 10 MM ZNCL2, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 6, 2009 / Details: mirror
RadiationMonochromator: Si-111 crystal Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 53606 / Num. obs: 53606 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 14.4
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / Num. unique all: 7783 / Rsym value: 0.49 / % possible all: 96.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1S

1u1s


Resolution: 2.05→30 Å / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 2725 5.09 %RANDOM
Rwork0.1994 ---
obs0.2026 53561 97.32 %-
all-53606 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.283 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 34.49 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 14 335 6911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056679
X-RAY DIFFRACTIONf_angle_d0.9039059
X-RAY DIFFRACTIONf_dihedral_angle_d13.9872537
X-RAY DIFFRACTIONf_chiral_restr0.0591092
X-RAY DIFFRACTIONf_plane_restr0.0041135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08730.39341270.2962704X-RAY DIFFRACTION96
2.0873-2.12740.35561460.29762628X-RAY DIFFRACTION97
2.1274-2.17080.34361450.26132614X-RAY DIFFRACTION96
2.1708-2.2180.32531360.23322733X-RAY DIFFRACTION96
2.218-2.26960.27591160.21972649X-RAY DIFFRACTION97
2.2696-2.32630.29571380.20712649X-RAY DIFFRACTION97
2.3263-2.38920.32521520.21512682X-RAY DIFFRACTION97
2.3892-2.45950.31821580.21512652X-RAY DIFFRACTION97
2.4595-2.53880.30821440.22842664X-RAY DIFFRACTION98
2.5388-2.62950.38351370.23042696X-RAY DIFFRACTION97
2.6295-2.73470.32111440.22422639X-RAY DIFFRACTION97
2.7347-2.85910.29681570.20542678X-RAY DIFFRACTION97
2.8591-3.00970.2711470.20462693X-RAY DIFFRACTION98
3.0097-3.1980.2531440.18732676X-RAY DIFFRACTION98
3.198-3.44460.28411500.20442686X-RAY DIFFRACTION98
3.4446-3.79060.25031350.18122681X-RAY DIFFRACTION98
3.7906-4.33760.22161420.17452713X-RAY DIFFRACTION98
4.3376-5.45920.17881610.15322714X-RAY DIFFRACTION98
5.4592-29.4050.21861460.18292685X-RAY DIFFRACTION98

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