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- PDB-7og8: Wild-type Hfq protein from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 7og8
TitleWild-type 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 serogroup C / serotype 2a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMoche, M. / Karlsson, J. / Loh, E.
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 6, 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)7,6771
Polymers7,6771
Non-polymers00
Water95553
1
A: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)46,0616
Polymers46,0616
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 area9440 Å2
ΔGint-69 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.539, 60.539, 27.476
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-151-

HOH

21A-152-

HOH

31A-153-

HOH

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Components

#1: Protein RNA-binding protein Hfq


Mass: 7676.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18) (bacteria)
Strain: ATCC 700532 / DSM 15464 / FAM18 / Gene: hfq, NMC0702 / Production host: Escherichia coli (E. coli) / References: UniProt: A1KT11
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: PEG3350, sodium nitrate, glycerol, bis-tris propane
PH range: 6.1-7.4

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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
ReflectionResolution: 1.4→30.27 Å / Num. obs: 11543 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Net I/σ(I): 13.7 / Num. measured all: 211386 / Scaling rejects: 1406
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
1.4-1.4216.91.20596305690.710.3011.2422.2100
7.67-30.2717.50.0821489850.9970.020.0853899

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
DIALS2.2.5data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNO

4pno


Resolution: 1.4→20.35 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 1.56 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 585 5.1 %RANDOM
Rwork0.246 ---
obs0.2477 10943 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.97 Å2 / Biso mean: 14.642 Å2 / Biso min: 6.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å2-0 Å2
2---0.09 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 1.4→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms539 0 0 53 592
Biso mean---26.81 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013555
X-RAY DIFFRACTIONr_bond_other_d0.0020.017533
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.631755
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5671236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2222.96327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3051599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.36153
X-RAY DIFFRACTIONr_chiral_restr0.0840.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02107
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 45 -
Rwork0.276 803 -
all-848 -
obs--99.88 %

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