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- PDB-7x2r: Crystal structure of the E. coli transcription termination factor Rho -

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Basic information

Entry
Database: PDB / ID: 7x2r
TitleCrystal structure of the E. coli transcription termination factor Rho
ComponentsTranscription termination factor Rho
KeywordsTRANSCRIPTION / E. coli transcription termination factor / TRANSLATION / HYDROLASE
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / RNA binding / ATP binding / cytosol
Similarity search - Function
Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain ...Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsZheng, J. / Wang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21773014 China
CitationJournal: To Be Published
Title: E. coli transcription termination factor Rho
Authors: Wang, B. / Zheng, J.
History
DepositionFeb 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription termination factor Rho
B: Transcription termination factor Rho
C: Transcription termination factor Rho
D: Transcription termination factor Rho
E: Transcription termination factor Rho
F: Transcription termination factor Rho


Theoretical massNumber of molelcules
Total (without water)282,4216
Polymers282,4216
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.496, 101.471, 204.818
Angle α, β, γ (deg.)90.000, 102.685, 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_1chain "A"
d_2ens_1(chain "B" and (resid 1 through 280 or resid 284 through 417))
d_3ens_1chain "C"
d_4ens_1(chain "D" and (resid 1 through 280 or resid 284 through 417))
d_5ens_1chain "E"
d_6ens_1(chain "F" and (resid 1 through 126 or resid 129 through 280 or resid 284 through 417))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLYSA1 - 408
d_21ens_1METALAB1 - 274
d_22ens_1VALLYSB278 - 411
d_31ens_1METLYSC1 - 408
d_41ens_1METALAD1 - 274
d_42ens_1VALLYSD276 - 409
d_51ens_1METLYSE1 - 408
d_61ens_1METASNF1 - 126
d_62ens_1ASNALAF129 - 276
d_63ens_1VALLYSF280 - 413

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Components

#1: Protein
Transcription termination factor Rho / ATP-dependent helicase Rho


Mass: 47070.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Gene: rho, NCTC10429_00403 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A377BS88, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4 M potassium chloride, 0.05 M magnesium chloride, 50 mM Tris pH 7.5, 13% (w/v) polyethylene glycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.988 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Nov 1, 2017
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 4.4→20 Å / Num. obs: 170098 / % possible obs: 86 % / Redundancy: 5 % / Biso Wilson estimate: 43.88 Å2 / CC1/2: 0.8 / Net I/σ(I): 0.8
Reflection shellResolution: 4.4→4.53 Å / Num. unique obs: 7 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XAV

6xav


Resolution: 4.4→19.99 Å / SU ML: 0.6051 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3148 1700 10 %
Rwork0.2723 15292 -
obs0.2765 16992 83.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.31 Å2
Refinement stepCycle: LAST / Resolution: 4.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19308 0 0 0 19308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004719581
X-RAY DIFFRACTIONf_angle_d1.089126360
X-RAY DIFFRACTIONf_chiral_restr0.05633031
X-RAY DIFFRACTIONf_plane_restr0.0083421
X-RAY DIFFRACTIONf_dihedral_angle_d18.46862641
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.76189770997
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.6771508747
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.7088699896
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.70067001415
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS2.37024945071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4-4.530.32161360.28371221X-RAY DIFFRACTION79.54
4.53-4.670.3671290.29331173X-RAY DIFFRACTION78.91
4.67-4.840.33321350.28141210X-RAY DIFFRACTION80.06
4.84-5.030.29771350.28351226X-RAY DIFFRACTION80.87
5.03-5.250.35831360.29961215X-RAY DIFFRACTION79.85
5.25-5.520.36471310.31511176X-RAY DIFFRACTION78.12
5.52-5.860.37281350.29831210X-RAY DIFFRACTION79.96
5.86-6.30.32731330.30671196X-RAY DIFFRACTION78.22
6.3-6.910.3651400.30151266X-RAY DIFFRACTION84.09
6.91-7.860.32551550.29081398X-RAY DIFFRACTION90.4
7.86-9.710.24281630.22031462X-RAY DIFFRACTION96.38
9.71-19.990.25061720.21711539X-RAY DIFFRACTION97.66

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