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- PDB-6wa8: Crystal structure of the E. coli transcription termination factor Rho -

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Basic information

Entry
Database: PDB / ID: 6wa8
TitleCrystal structure of the E. coli transcription termination factor Rho
ComponentsTranscription termination factor Rho
KeywordsTRANSCRIPTION / Hydrolase / ATPase
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / DNA-templated transcription termination / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / 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 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFan, C. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the Escherichia coli transcription termination factor Rho.
Authors: Fan, C. / Rees, D.C.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,46412
Polymers282,4216
Non-polymers3,0436
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.745, 101.902, 184.016
Angle α, β, γ (deg.)90.000, 107.770, 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-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLY(chain 'B' and (resid 1 through 23 or resid 25...BB1 - 221 - 22
12ASNASNSERSER(chain 'B' and (resid 1 through 23 or resid 25...BB25 - 4525 - 45
13ASPASPPROPRO(chain 'B' and (resid 1 through 23 or resid 25...BB48 - 10348 - 103
14TYRTYRPHEPHE(chain 'B' and (resid 1 through 23 or resid 25...BB110 - 121110 - 121
15LYSLYSPROPRO(chain 'B' and (resid 1 through 23 or resid 25...BB130 - 138130 - 138
16SERSERMETMET(chain 'B' and (resid 1 through 23 or resid 25...BB143 - 147143 - 147
17GLYGLYALAALA(chain 'B' and (resid 1 through 23 or resid 25...BB152 - 182152 - 182
18THRTHRLEULEU(chain 'B' and (resid 1 through 23 or resid 25...BB185 - 222185 - 222
19GLYGLYPROPRO(chain 'B' and (resid 1 through 23 or resid 25...BB225 - 279225 - 279
110VALVALILEILE(chain 'B' and (resid 1 through 23 or resid 25...BB284 - 349284 - 349
111VALVALMETMET(chain 'B' and (resid 1 through 23 or resid 25...BB354 - 390354 - 390
112ASPASPMETMET(chain 'B' and (resid 1 through 23 or resid 25...BB394 - 405394 - 405
21METMETGLYGLY(chain 'C' and (resid 1 through 23 or resid 25...CC1 - 221 - 22
22ASNASNSERSER(chain 'C' and (resid 1 through 23 or resid 25...CC25 - 4525 - 45
23ASPASPPROPRO(chain 'C' and (resid 1 through 23 or resid 25...CC48 - 10348 - 103
24TYRTYRPHEPHE(chain 'C' and (resid 1 through 23 or resid 25...CC110 - 121110 - 121
25LYSLYSPROPRO(chain 'C' and (resid 1 through 23 or resid 25...CC130 - 138130 - 138
26SERSERMETMET(chain 'C' and (resid 1 through 23 or resid 25...CC143 - 147143 - 147
27GLYGLYALAALA(chain 'C' and (resid 1 through 23 or resid 25...CC152 - 182152 - 182
28THRTHRLEULEU(chain 'C' and (resid 1 through 23 or resid 25...CC185 - 222185 - 222
29GLYGLYPROPRO(chain 'C' and (resid 1 through 23 or resid 25...CC225 - 279225 - 279
210VALVALILEILE(chain 'C' and (resid 1 through 23 or resid 25...CC284 - 349284 - 349
211VALVALMETMET(chain 'C' and (resid 1 through 23 or resid 25...CC354 - 390354 - 390
212ASPASPMETMET(chain 'C' and (resid 1 through 23 or resid 25...CC394 - 405394 - 405
31METMETGLYGLY(chain 'D' and (resid 1 through 23 or resid 25...DD1 - 221 - 22
32ASNASNSERSER(chain 'D' and (resid 1 through 23 or resid 25...DD25 - 4525 - 45
33ASPASPPROPRO(chain 'D' and (resid 1 through 23 or resid 25...DD48 - 10348 - 103
34TYRTYRPHEPHE(chain 'D' and (resid 1 through 23 or resid 25...DD110 - 121110 - 121
35LYSLYSPROPRO(chain 'D' and (resid 1 through 23 or resid 25...DD130 - 138130 - 138
36SERSERMETMET(chain 'D' and (resid 1 through 23 or resid 25...DD143 - 147143 - 147
37GLYGLYALAALA(chain 'D' and (resid 1 through 23 or resid 25...DD152 - 182152 - 182
38THRTHRLEULEU(chain 'D' and (resid 1 through 23 or resid 25...DD185 - 222185 - 222
39GLYGLYPROPRO(chain 'D' and (resid 1 through 23 or resid 25...DD225 - 279225 - 279
310VALVALILEILE(chain 'D' and (resid 1 through 23 or resid 25...DD284 - 349284 - 349
311VALVALMETMET(chain 'D' and (resid 1 through 23 or resid 25...DD354 - 390354 - 390
312ASPASPMETMET(chain 'D' and (resid 1 through 23 or resid 25...DD394 - 405394 - 405
41METMETGLYGLY(chain 'E' and (resid 1 through 23 or resid 25...EE1 - 221 - 22
42ASNASNSERSER(chain 'E' and (resid 1 through 23 or resid 25...EE25 - 4525 - 45
43ASPASPPROPRO(chain 'E' and (resid 1 through 23 or resid 25...EE48 - 10348 - 103
44TYRTYRPHEPHE(chain 'E' and (resid 1 through 23 or resid 25...EE110 - 121110 - 121
45LYSLYSPROPRO(chain 'E' and (resid 1 through 23 or resid 25...EE130 - 138130 - 138
46SERSERMETMET(chain 'E' and (resid 1 through 23 or resid 25...EE143 - 147143 - 147
47GLYGLYALAALA(chain 'E' and (resid 1 through 23 or resid 25...EE152 - 182152 - 182
48THRTHRLEULEU(chain 'E' and (resid 1 through 23 or resid 25...EE185 - 222185 - 222
49GLYGLYPROPRO(chain 'E' and (resid 1 through 23 or resid 25...EE225 - 279225 - 279
410VALVALILEILE(chain 'E' and (resid 1 through 23 or resid 25...EE284 - 349284 - 349
411VALVALMETMET(chain 'E' and (resid 1 through 23 or resid 25...EE354 - 390354 - 390
412ASPASPMETMET(chain 'E' and (resid 1 through 23 or resid 25...EE394 - 405394 - 405
51METMETGLYGLY(chain 'F' and (resid 1 through 23 or resid 25...FF1 - 221 - 22
52ASNASNSERSER(chain 'F' and (resid 1 through 23 or resid 25...FF25 - 4525 - 45
53ASPASPPROPRO(chain 'F' and (resid 1 through 23 or resid 25...FF48 - 10348 - 103
54TYRTYRPHEPHE(chain 'F' and (resid 1 through 23 or resid 25...FF110 - 121110 - 121
55LYSLYSPROPRO(chain 'F' and (resid 1 through 23 or resid 25...FF130 - 138130 - 138
56SERSERMETMET(chain 'F' and (resid 1 through 23 or resid 25...FF143 - 147143 - 147
57GLYGLYALAALA(chain 'F' and (resid 1 through 23 or resid 25...FF152 - 182152 - 182
58THRTHRLEULEU(chain 'F' and (resid 1 through 23 or resid 25...FF185 - 222185 - 222
59GLYGLYPROPRO(chain 'F' and (resid 1 through 23 or resid 25...FF225 - 279225 - 279
510VALVALILEILE(chain 'F' and (resid 1 through 23 or resid 25...FF284 - 349284 - 349
511VALVALMETMET(chain 'F' and (resid 1 through 23 or resid 25...FF354 - 390354 - 390
512ASPASPMETMET(chain 'F' and (resid 1 through 23 or resid 25...FF394 - 405394 - 405

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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 (strain K12) (bacteria)
Strain: K12 / Gene: rho, nitA, psuA, rnsC, sbaA, tsu, b3783, JW3756 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AG30, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 100 mM NaCl, 100 mM Tris pH 8.3, 28% PEG2000MME, 20 mM ATP, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→39.79 Å / Num. obs: 43015 / % possible obs: 99.61 % / Redundancy: 7 % / Biso Wilson estimate: 88.34 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.2058 / Rpim(I) all: 0.08388 / Rrim(I) all: 0.2225 / Net I/σ(I): 8.92
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 4146 / CC1/2: 0.55 / CC star: 0.842 / Rpim(I) all: 0.5969 / Rrim(I) all: 1.551 / % possible all: 97.32

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PVO

1pvo


Resolution: 3.3→39.79 Å / SU ML: 0.4931 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2961 2095 4.88 %
Rwork0.2515 40807 -
obs0.2537 42902 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19590 0 186 0 19776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001820080
X-RAY DIFFRACTIONf_angle_d0.575827092
X-RAY DIFFRACTIONf_chiral_restr0.04243080
X-RAY DIFFRACTIONf_plane_restr0.00373502
X-RAY DIFFRACTIONf_dihedral_angle_d15.02962780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.380.34181330.32522571X-RAY DIFFRACTION96.16
3.38-3.460.3871460.30742710X-RAY DIFFRACTION99.79
3.46-3.550.32181410.30962712X-RAY DIFFRACTION99.96
3.56-3.660.38381520.31612691X-RAY DIFFRACTION99.93
3.66-3.780.38911190.30792734X-RAY DIFFRACTION99.93
3.78-3.910.30551430.28662714X-RAY DIFFRACTION100
3.91-4.070.32181330.2662721X-RAY DIFFRACTION100
4.07-4.250.24361460.25532720X-RAY DIFFRACTION100
4.25-4.480.29171570.24012711X-RAY DIFFRACTION99.97
4.48-4.760.2931410.22292734X-RAY DIFFRACTION100
4.76-5.120.28451220.22392727X-RAY DIFFRACTION100
5.12-5.640.33381500.25752740X-RAY DIFFRACTION100
5.64-6.450.29911450.2672736X-RAY DIFFRACTION100
6.45-8.120.26681300.252775X-RAY DIFFRACTION100
8.12-39.790.23141370.19292811X-RAY DIFFRACTION99.46
Refinement TLS params.Method: refined / Origin x: 22.6940334532 Å / Origin y: -12.8189458953 Å / Origin z: 43.4903218321 Å
111213212223313233
T0.483160583526 Å2-0.0215539646395 Å20.228949238256 Å2-0.463452880973 Å20.0082716642686 Å2--0.722635441431 Å2
L0.488541147526 °2-0.0543749354777 °2-0.164981782135 °2-0.253709993025 °20.0275314950275 °2--0.710334472196 °2
S0.0878177888481 Å °-0.0572394576712 Å °-0.124970982765 Å °0.0630852984348 Å °-0.0489240869261 Å °0.0313244840754 Å °0.031145669381 Å °-0.0389921988324 Å °-0.0402626518729 Å °
Refinement TLS groupSelection details: all

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