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- PDB-7oh8: R17A mutant of Hfq protein from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 7oh8
TitleR17A 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: 1.7 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 9, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)22,7723
Polymers22,7723
Non-polymers00
Water3,981221
1
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq

A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)45,5456
Polymers45,5456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9400 Å2
ΔGint-70 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.683, 106.252, 27.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-169-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA5 - 701 - 66
21VALVALBB5 - 701 - 66
12VALVALAA5 - 701 - 66
22VALVALCC5 - 701 - 66
13LEULEUBB5 - 721 - 68
23LEULEUCC5 - 721 - 68

NCS ensembles :
ID
1
2
3

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Components

#1: Protein RNA-binding protein Hfq


Mass: 7590.796 Da / Num. of mol.: 3 / Mutation: R17A
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.: 221 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 1500, SPG pH 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: 1.7→40.25 Å / Num. obs: 21006 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.071 / Rrim(I) all: 0.255 / Net I/σ(I): 9.4 / Num. measured all: 268092 / Scaling rejects: 19
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
1.7-1.7312.32.041324410770.5660.5962.1281.496.1
9-40.2510.10.04818861860.9990.0150.0513299.2

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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: 4PN0

4pn0


Resolution: 1.7→30.86 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.873 / SU B: 4.215 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1636 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 991 4.9 %RANDOM
Rwork0.2405 ---
obs0.2432 19372 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.38 Å2 / Biso mean: 19.47 Å2 / Biso min: 9.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.7→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 0 222 1813
Biso mean---31.47 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171560
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.6292228
X-RAY DIFFRACTIONr_angle_other_deg1.3331.5653621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68724.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34715285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.333156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A19600.08
12B19600.08
21A19630.08
22C19630.08
31B20100.05
32C20100.05
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 72 -
Rwork0.291 1431 -
all-1503 -
obs--96.97 %

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