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- PDB-8p91: Hfq from Chromobacterium haemolyticum; a P6 space group monomer -

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Basic information

Entry
Database: PDB / ID: 8p91
TitleHfq from Chromobacterium haemolyticum; a P6 space group monomer
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / Hfq / translation regulation
Function / homologyRNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily / regulation of DNA-templated transcription / RNA binding / RNA-binding protein Hfq
Function and homology information
Biological speciesChromobacterium haemolyticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNikulin, A.D. / Lekontseva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and Science of the Russian Federation Russian Federation
CitationJournal: Crystallography Reports
Title: Hfq from Chromobacterium haemolyticum
Authors: Nikulin, A.D. / Lekontseva, N.V.
History
DepositionJun 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.entity_id_list
Revision 1.2Mar 13, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI

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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)9,6901
Polymers9,6901
Non-polymers00
Water2,000111
1
A: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)58,1416
Polymers58,1416
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 area9670 Å2
ΔGint-75 kcal/mol
Surface area18280 Å2
Unit cell
Length a, b, c (Å)65.145, 65.145, 27.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein RNA-binding protein Hfq


Mass: 9690.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium haemolyticum (bacteria)
Gene: hfq, B0T39_13335, B0T45_12055, CH06BL_33310, DBB33_18715
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): E. coli / References: UniProt: A0A1W0CX06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.75 Å3/Da / Density % sol: 29.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: #23 of JBScreen Nuc-Pro 1 (Jena Bioscience) 15% PEG4000, 50 mM Tris-HCl, pH 7.5, 150 mM KCl, 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→21.32 Å / Num. obs: 13426 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.045 / Rrim(I) all: 0.106 / Χ2: 0.96 / Net I/σ(I): 10.7 / Num. measured all: 68788
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.73 / Num. measured all: 2424 / Num. unique obs: 663 / CC1/2: 0.478 / Rpim(I) all: 0.442 / Rrim(I) all: 0.856 / Χ2: 0.88 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
Aimlessdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→21.32 Å / Cross valid method: FREE R-VALUE / σ(F): 38.87 / Phase error: 30.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 682 5.08 %5%
Rwork0.1549 ---
obs0.169 13426 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.16 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 1 115 650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006557
X-RAY DIFFRACTIONf_angle_d0.909760
X-RAY DIFFRACTIONf_dihedral_angle_d5.51575
X-RAY DIFFRACTIONf_chiral_restr0.08792
X-RAY DIFFRACTIONf_plane_restr0.00696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.510.23311220.21472532X-RAY DIFFRACTION95
1.51-1.660.19741200.1782520X-RAY DIFFRACTION95
1.66-1.90.19331560.16632521X-RAY DIFFRACTION94
1.9-2.390.19751320.16162552X-RAY DIFFRACTION95
2.39-21.320.19431520.15682619X-RAY DIFFRACTION95

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