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- PDB-2oug: Crystal structure of the RfaH transcription factor at 2.1A resolution -

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Basic information

Entry
Database: PDB / ID: 2oug
TitleCrystal structure of the RfaH transcription factor at 2.1A resolution
ComponentsTranscriptional activator rfaH
KeywordsTRANSCRIPTION / transcription factor / virulence / transcription pausing / transcription elongation
Function / homology
Function and homology information


regulatory RNA binding / transcription antitermination factor activity, DNA binding / translation activator activity / DNA-templated transcription elongation / transcription elongation-coupled chromatin remodeling / bacterial-type RNA polymerase core enzyme binding / positive regulation of translation / transcription antitermination / DNA binding / cytosol
Similarity search - Function
NusG, N-terminal domain / Transcription antitermination protein RfaH / NusG-like / Transcription 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription antitermination protein RfaH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsVassylyev, D.G. / Vassylyeva, M.N. / Svetlov, V. / Artsimovitch, I.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for converting a general transcription factor into an operon-specific virulence regulator.
Authors: Belogurov, G.A. / Vassylyeva, M.N. / Svetlov, V. / Klyuyev, S. / Grishin, N.V. / Vassylyev, D.G. / Artsimovitch, I.
History
DepositionFeb 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator rfaH
B: Transcriptional activator rfaH
C: Transcriptional activator rfaH
D: Transcriptional activator rfaH


Theoretical massNumber of molelcules
Total (without water)73,4574
Polymers73,4574
Non-polymers00
Water8,593477
1
A: Transcriptional activator rfaH


Theoretical massNumber of molelcules
Total (without water)18,3641
Polymers18,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional activator rfaH


Theoretical massNumber of molelcules
Total (without water)18,3641
Polymers18,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional activator rfaH


Theoretical massNumber of molelcules
Total (without water)18,3641
Polymers18,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional activator rfaH


Theoretical massNumber of molelcules
Total (without water)18,3641
Polymers18,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.149, 45.149, 600.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is a monomer

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Components

#1: Protein
Transcriptional activator rfaH


Mass: 18364.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaH, hlyT, sfrB / Plasmid: pVS12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (lambdaDE3) / References: UniProt: P0AFW0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG MME 5000, 50mM sodium cacodylate, 20 mM Co chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 38387 / Num. obs: 38387 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 27.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3238 / Rsym value: 0.497 / % possible all: 76.7

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Processing

Software
NameVersionClassification
MAR345data collection
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED ...Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED OUT USING THE TWINNING OPTION OF THE CNS PROGRAM. FOR THE DEPOSITION THE DIFFRACTION DATA WERE DETWINNED USING THE CNS PROGRAM. THEREFORE, SOME REFLECTIONS WERE LOST DUE TO THE DETWINNING PROCEDURE AND ARE MISSING IN THE DEPOSITED SF FILE, WHEREAS THE REFINEMENT STATISTICS CALCULATED BASED ON THE DETWINNED DATA MIGHT BE SLIGHTLY DIFFERENT FROM THOSE OBTAINED DURING THE "TWINNED" REFINEMENT INCLUDED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2091 -random
Rwork0.238 ---
all0.242 38387 --
obs0.242 38387 93.8 %-
Displacement parametersBiso mean: 43.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 0 477 4981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.336 151 -
Rwork0.332 --
obs-3238 76.7 %

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