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- PDB-1grj: GREA TRANSCRIPT CLEAVAGE FACTOR FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1grj
TitleGREA TRANSCRIPT CLEAVAGE FACTOR FROM ESCHERICHIA COLI
ComponentsGREA PROTEIN
KeywordsTRANSCRIPTION REGULATION / TRANSCRIPT ELONGATION FACTOR / TRANSCRIPT CLEAVAGE FACTOR
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / DNA-templated transcription elongation / RNA polymerase binding / regulation of DNA-templated transcription elongation / DNA binding / cytoplasm / cytosol
Similarity search - Function
Transcription elongation factor GreA / Transcription elongation factor GreA/GreB / Prokaryotic transcription elongation factors signature 1. / Transcription elongation factor, GreA/GreB, N-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, conserved site / Transcription elongation factor, GreA/GreB, N-terminal / Transcription elongation factor, GreA/GreB, N-terminal domain superfamily / Transcription elongation factor, N-terminal / Prokaryotic transcription elongation factors signature 2. ...Transcription elongation factor GreA / Transcription elongation factor GreA/GreB / Prokaryotic transcription elongation factors signature 1. / Transcription elongation factor, GreA/GreB, N-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, conserved site / Transcription elongation factor, GreA/GreB, N-terminal / Transcription elongation factor, GreA/GreB, N-terminal domain superfamily / Transcription elongation factor, N-terminal / Prokaryotic transcription elongation factors signature 2. / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Chitinase A; domain 3 / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor GreA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsDarst, S.A. / Stebbins, C.E.
Citation
Journal: Nature / Year: 1995
Title: Crystal structure of the GreA transcript cleavage factor from Escherichia coli.
Authors: Stebbins, C.E. / Borukhov, S. / Orlova, M. / Polyakov, A. / Goldfarb, A. / Darst, S.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Grea, a Transcript Cleavage Factor from Escherichia Coli
Authors: Darst, S.A. / Stebbins, C.E. / Borukhov, S. / Orlova, M. / Feng, G. / Landick, R. / Goldfarb, A.
History
DepositionMay 2, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREA PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,6631
Polymers17,6631
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.357, 42.660, 39.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GREA PROTEIN


Mass: 17662.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: XL1-BLUE / References: UniProt: P0A6W5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-20 %(w/v)PEG80001reservoir
20.2 M1reservoirCaCl2
310 mMdithiothreitol1reservoir
40.1 MMES1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.5418
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 8079 / Observed criterion σ(I): 1 / Redundancy: 15.1 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
% possible obs: 85.5 % / Redundancy: 3.8 % / Num. measured all: 30813 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.32 -0.1 %
Rwork0.209 --
obs0.209 8040 86 %
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 294 1749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.1
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_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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