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- PDB-7ogw: Q9A mutant of Hfq protein from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 7ogw
TitleQ9A mutant of Hfq protein from Neisseria meningitidis
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / sRNA / mRNA / annealing
Function / homologyRNA-binding protein Hfq / Hfq protein / LSM domain superfamily / regulation of DNA-templated transcription / RNA binding / RNA-binding protein Hfq
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsMoche, M. / Karlsson, J. / Loh, E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2014.0177 Sweden
CitationJournal: To Be Published
Title: Crystal structures of wild type, Q9A and R17A single mutant Hfq structures from Neisseria meningitidis
Authors: Karlsson, J. / Moche, M. / Loh, E.
History
DepositionMay 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)7,6201
Polymers7,6201
Non-polymers00
Water2,270126
1
A: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)45,7196
Polymers45,7196
Non-polymers00
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 area9220 Å2
ΔGint-73 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.175, 62.175, 27.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-176-

HOH

21A-202-

HOH

31A-220-

HOH

41A-224-

HOH

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Components

#1: Protein RNA-binding protein Hfq


Mass: 7619.860 Da / Num. of mol.: 1 / Mutation: Q9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: hfq, COH33_00770, COH52_02035, COI31_11405, ERS514851_00105, JY21_08770
Production host: Escherichia coli (E. coli) / References: UniProt: B9VV05
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG3350, sodium nitrate, bis-tris propane / PH range: 6.5-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.313
11-K, -H, -L20.687
ReflectionResolution: 1.09→31.09 Å / Num. obs: 25701 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.013 / Rrim(I) all: 0.056 / Net I/σ(I): 30 / Num. measured all: 489717 / Scaling rejects: 66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.09-1.1117.60.5292201812540.9310.1270.5455.699.4
5.97-31.0918.50.04332861780.9990.010.04470.498.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDS20210323data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNO

4pno


Resolution: 1.09→27.71 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.441 / SU ML: 0.011 / SU R Cruickshank DPI: 0.0046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.005 / ESU R Free: 0.005 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1176 1281 5 %RANDOM
Rwork0.1009 ---
obs0.1017 24415 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.41 Å2 / Biso mean: 13.814 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å20 Å2
2--3.87 Å20 Å2
3----7.74 Å2
Refinement stepCycle: final / Resolution: 1.09→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms535 0 0 129 664
Biso mean---28.32 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.013560
X-RAY DIFFRACTIONr_bond_other_d0.0030.017536
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.63764
X-RAY DIFFRACTIONr_angle_other_deg1.551.5671243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.412571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18322.96327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2491598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.368153
X-RAY DIFFRACTIONr_chiral_restr0.1360.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02624
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02109
X-RAY DIFFRACTIONr_rigid_bond_restr5.44431096
LS refinement shellResolution: 1.091→1.119 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.116 97 -
Rwork0.091 1767 -
all-1864 -
obs--99.52 %

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