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- PDB-2eyq: Crystal structure of Escherichia coli transcription-repair coupli... -

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Basic information

Entry
Database: PDB / ID: 2eyq
TitleCrystal structure of Escherichia coli transcription-repair coupling factor
ComponentsTranscription-repair coupling factor
KeywordsHYDROLASE / Mfd / SF2 ATPase
Function / homology
Function and homology information


transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / DNA repair complex / transcription-coupled nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / hydrolase activity / DNA repair ...transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / DNA repair complex / transcription-coupled nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / hydrolase activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / DNA binding / ATP binding / cytosol
Similarity search - Function
Rossmann fold - #11180 / Rossmann fold - #11140 / Transcription-repair-coupling factor, D7 domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / : / MFD, D3 domain / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain ...Rossmann fold - #11180 / Rossmann fold - #11140 / Transcription-repair-coupling factor, D7 domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / : / MFD, D3 domain / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / : / UvrB, interaction domain / UvrB interaction domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / Thrombin, subunit H - #170 / Aspartate Aminotransferase, domain 1 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription-repair-coupling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsDeaconescu, A.M. / Darst, S.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural basis for bacterial transcription-coupled DNA repair.
Authors: Deaconescu, A.M. / Chambers, A.L. / Smith, A.J. / Nickels, B.E. / Hochschild, A. / Savery, N.J. / Darst, S.A.
History
DepositionNov 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription-repair coupling factor
B: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,36910
Polymers260,8902
Non-polymers1,4808
Water2,162120
1
A: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1135
Polymers130,4451
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2565
Polymers130,4451
Non-polymers8114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.870, 161.990, 161.730
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription-repair coupling factor / TRCF


Mass: 130444.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mfd / Production host: Escherichia coli (E. coli) / References: UniProt: P30958
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% pentaerythritol ethoxylate 100 mM HEPES, pH 7.5 75mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98166 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98166 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 61409 / % possible obs: 99.9 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3.2→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 3083 RANDOM
Rwork0.234 --
all0.234 62228 -
obs0.234 61185 -
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17853 0 90 120 18063

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