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- PDB-8f5g: NusG-RNA complex -

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Basic information

Entry
Database: PDB / ID: 8f5g
TitleNusG-RNA complex
Components
  • RNA
  • Transcription termination/antitermination protein NusG
KeywordsRNA BINDING PROTEIN/RNA / KOW domain / Transcription / RNA-binding protein / Regulatory RNA / RNA BINDING PROTEIN-RNA complex
Function / homologyDI(HYDROXYETHYL)ETHER / RNA / RNA (> 10)
Function and homology information
Biological speciesThermoanaerobacter pseudethanolicus (bacteria)
Bacillus velezensis FZB42 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsElghondakly, A.T. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: NusG-RNA complex
Authors: Elghondakly, A.T. / Ferre-D'Amare, A.R.
History
DepositionNov 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA
A: Transcription termination/antitermination protein NusG
E: RNA
B: Transcription termination/antitermination protein NusG
F: RNA
C: Transcription termination/antitermination protein NusG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8057
Polymers88,6996
Non-polymers1061
Water1,09961
1
D: RNA
A: Transcription termination/antitermination protein NusG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6733
Polymers29,5662
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: RNA
B: Transcription termination/antitermination protein NusG


Theoretical massNumber of molelcules
Total (without water)29,5662
Polymers29,5662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: RNA
C: Transcription termination/antitermination protein NusG


Theoretical massNumber of molelcules
Total (without water)29,5662
Polymers29,5662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.951, 87.451, 148.793
Angle α, β, γ (deg.)90.000, 103.240, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 9 or (resid 10...
d_2ens_1(chain "C" and (resid 0 through 2 or (resid 3...
d_1ens_2chain "D"
d_2ens_2chain "E"
d_3ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRALAB2 - 91
d_12ens_1VALLYSB93 - 142
d_13ens_1LYSASNB144 - 169
d_21ens_1THRALAG1 - 90
d_22ens_1VALLYSG92 - 141
d_23ens_1LYSASNG143 - 168
d_11ens_2GCA
d_21ens_2GCD
d_31ens_2GCF

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.00985661338454, -0.75854826328, 0.651542308256), (0.729286163464, -0.451241231523, -0.514318036581), (0.684137806989, 0.47009135628, 0.557646463092)-20.8817628563, -18.5981919487, -12.0760657406
2given(-0.122533414606, -0.695466639303, -0.708033696883), (-0.687288234732, -0.455199855203, 0.566063577897), (-0.715975170452, 0.555984932746, -0.422208846255)13.0452279527, -72.1305354468, 86.4465241589
3given(-0.0235711943408, -0.76074013789, 0.648628430923), (0.706376443498, -0.471796714688, -0.527674312508), (0.707443792021, 0.445737930418, 0.54848972508)-20.4091920688, -18.1031443209, -12.1344246117

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Components

#1: RNA chain RNA /


Mass: 8287.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Bacillus velezensis FZB42 (bacteria)
#2: Protein Transcription termination/antitermination protein NusG


Mass: 21278.475 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 0.25 M sodium acetate, pH 5.2, 12% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.7→48.28 Å / Num. obs: 23756 / % possible obs: 99.84 % / Redundancy: 12.5 % / Biso Wilson estimate: 56.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04819 / Net I/σ(I): 18.7
Reflection shellResolution: 2.7→2.79 Å / Rmerge(I) obs: 0.2725 / Num. unique obs: 2379 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.28 Å / SU ML: 0.3816 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 1505 6.34 %
Rwork0.2093 22251 -
obs0.2122 23756 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.52 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 1641 7 61 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195599
X-RAY DIFFRACTIONf_angle_d0.47627910
X-RAY DIFFRACTIONf_chiral_restr0.0388985
X-RAY DIFFRACTIONf_plane_restr0.0032706
X-RAY DIFFRACTIONf_dihedral_angle_d12.58162344
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS2.47894723876
ens_2d_2AX-RAY DIFFRACTIONTorsion NCS0.298973237165
ens_2d_3AX-RAY DIFFRACTIONTorsion NCS0.56795588488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.790.34431390.2882028X-RAY DIFFRACTION100
2.79-2.890.39321340.27891999X-RAY DIFFRACTION100
2.89-30.33751360.26561988X-RAY DIFFRACTION100
3-3.140.26821330.24222072X-RAY DIFFRACTION99.95
3.14-3.30.29631390.24032008X-RAY DIFFRACTION100
3.3-3.510.24241370.2211994X-RAY DIFFRACTION99.81
3.51-3.780.28341350.21912000X-RAY DIFFRACTION99.3
3.78-4.160.26441380.19342011X-RAY DIFFRACTION99.58
4.16-4.760.19541350.17312016X-RAY DIFFRACTION100
4.76-60.21561350.19382044X-RAY DIFFRACTION99.95
6-48.280.23981440.18992091X-RAY DIFFRACTION99.87

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