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- PDB-1a62: CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONA... -

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Basic information

Entry
Database: PDB / ID: 1a62
TitleCRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TERMINATOR PROTEIN RHO
ComponentsRHO
KeywordsTRANSCRIPTION TERMINATION / TERMINATION / RNA BINDING DOMAIN / TRANSCRIPTION REGULATION / OB FOLD / F1-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 / hydrolase activity / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transcription termination factor Rho / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsAllison, T.J. / Wood, T.C. / Briercheck, D.M. / Rastinejad, F. / Richardson, J.P. / Rule, G.S.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of the RNA-binding domain from transcription termination factor rho.
Authors: Allison, T.J. / Wood, T.C. / Briercheck, D.M. / Rastinejad, F. / Richardson, J.P. / Rule, G.S.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: The NMR Structure of the RNA Binding Domain of E. Coli Rho Factor Suggests Possible RNA-Protein Interactions
Authors: Briercheck, D.M. / Wood, T.C. / Allison, T.J. / Richardson, J.P. / Rule, G.S.
#2: Journal: J.Biomol.NMR / Year: 1996
Title: 1H, 15N and 13C Resonance Assignments and Secondary Structure Determination of the RNA-Binding Domain of E.Coli Rho Protein
Authors: Briercheck, D.M. / Allison, T.J. / Richardson, J.P. / Ellena, J.F. / Wood, T.C. / Rule, G.S.
History
DepositionMar 5, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHO


Theoretical massNumber of molelcules
Total (without water)14,7751
Polymers14,7751
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.950, 56.010, 42.920
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RHO


Mass: 14775.287 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN, RESIDUES 1 - 130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21 (DE3) / Cell line: BL21 / Plasmid: PET11A / Species (production host): Escherichia coli / Gene (production host): RHO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03002, UniProt: P0AG30*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 33 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein11
2200 mMpotassium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.969, 0.978, 0.979, 0.984
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9691
20.9781
30.9791
40.9841
ReflectionResolution: 1.55→30 Å / Num. obs: 16360 / % possible obs: 92 % / Observed criterion σ(I): 0.01 / Redundancy: 6 % / Rmerge(I) obs: 0.068 / Rsym value: 0.04 / Net I/σ(I): 22
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.26 / % possible all: 67
Reflection shell
*PLUS
% possible obs: 67 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.01
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1636 10 %RANDOM
Rwork0.216 ---
obs0.216 16360 92 %-
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 0 115 1103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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