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- PDB-9ik0: Crystal structure of PrfaH encoded by IncX3 plasmids -

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Basic information

Entry
Database: PDB / ID: 9ik0
TitleCrystal structure of PrfaH encoded by IncX3 plasmids
ComponentsTranscription antitermination protein RfaH
KeywordsTRANSCRIPTION / antiterminator
Function / homologyTranscription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / transcription elongation-coupled chromatin remodeling / Transcription antitermination protein RfaH
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, J. / Lu, Y. / Yu, J. / Cai, X. / Wang, C. / Lv, L. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2025
Title: Comprehensive analysis of Enterobacteriaceae IncX plasmids reveals robust conjugation regulators PrfaH, H-NS, and conjugation-fitness tradeoff.
Authors: Yang, J. / Lu, Y. / Yu, J. / Cai, X. / Wang, C. / Lv, L. / Moran, R.A. / Zhao, X. / Hu, Z. / Deng, M. / Liu, J.H.
History
DepositionJun 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription antitermination protein RfaH
B: Transcription antitermination protein RfaH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4974
Polymers37,3812
Non-polymers1162
Water4,594255
1
A: Transcription antitermination protein RfaH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7832
Polymers18,6901
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription antitermination protein RfaH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7152
Polymers18,6901
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.695, 57.695, 116.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Transcription antitermination protein RfaH


Mass: 18690.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaH, PMPNAOBH_00043 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A288W2P1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M Sodium citrate tribasic dihydrate pH 4.8, 15-18% w/v PEG20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→32.21 Å / Num. obs: 25086 / % possible obs: 97.62 % / Redundancy: 9.8 % / Biso Wilson estimate: 29.52 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06435 / Net I/σ(I): 23.4
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.5934 / Num. unique obs: 2361 / CC1/2: 0.903 / CC star: 0.974 / % possible all: 92.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2→32.21 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2142 1249 4.98 %
Rwork0.179 23820 -
obs0.1808 25069 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.41 Å2
Refinement stepCycle: LAST / Resolution: 2→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 7 255 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242619
X-RAY DIFFRACTIONf_angle_d0.53383553
X-RAY DIFFRACTIONf_chiral_restr0.0427377
X-RAY DIFFRACTIONf_plane_restr0.0056459
X-RAY DIFFRACTIONf_dihedral_angle_d13.4947980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.26511140.21822509X-RAY DIFFRACTION93.05
2.08-2.170.25311380.20632638X-RAY DIFFRACTION97.68
2.17-2.290.23131500.20622630X-RAY DIFFRACTION97.78
2.29-2.430.2484970.21732681X-RAY DIFFRACTION97.61
2.43-2.620.2471550.19522661X-RAY DIFFRACTION98.08
2.62-2.880.25451460.20292664X-RAY DIFFRACTION98.56
2.88-3.30.21281420.18412655X-RAY DIFFRACTION98.59
3.3-4.160.20351350.15792716X-RAY DIFFRACTION98.89
4.16-32.210.18051720.15382666X-RAY DIFFRACTION98.54

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