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- PDB-2b2n: Structure of transcription-repair coupling factor -

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Basic information

Entry
Database: PDB / ID: 2b2n
TitleStructure of transcription-repair coupling factor
ComponentsTranscription-repair coupling factor
KeywordsTRANSCRIPTION / DNA REPAIR / x-ray crystallography / strand-specific repair / template strand / RNA polymerase / RNAP / uvrA/B/C repair system
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 / 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 ...Rossmann fold - #11180 / 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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Transcription-repair-coupling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsAssenmacher, N. / Wenig, K. / Lammens, A. / Hopfner, K.-P.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Transcription-coupled Repair: the N Terminus of Mfd Resembles UvrB with Degenerate ATPase Motifs
Authors: Assenmacher, N. / Wenig, K. / Lammens, A. / Hopfner, K.-P.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)79,6058
Polymers78,7912
Non-polymers8146
Water7,800433
1
A: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7433
Polymers39,3961
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8625
Polymers39,3961
Non-polymers4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.650, 112.650, 213.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transcription-repair coupling factor / TRCF / Mfd protein


Mass: 39395.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mfd / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P30958
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O8
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, sodium citrate, ammonium sulfate, sodium formiate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97788, 0.9798, 0.97395
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2005
RadiationMonochromator: diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.977881
20.97981
30.973951
ReflectionResolution: 2.1→20 Å / Num. all: 47427 / Num. obs: 47377 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Rsym value: 0.084
Reflection shellResolution: 2.1→2.3 Å / Rsym value: 0.372 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ProDCdata collection
XDSdata reduction
SOLVEphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2376 5 %RANDOM
Rwork0.198 ---
all-47427 --
obs-47377 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.489 Å2-0.246 Å20 Å2
2--0.489 Å20 Å2
3----0.978 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 52 433 5462
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008979
X-RAY DIFFRACTIONc_angle_deg1.37603
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.4551.5
X-RAY DIFFRACTIONc_mcangle_it2.2582
X-RAY DIFFRACTIONc_scbond_it2.2292
X-RAY DIFFRACTIONc_scangle_it3.2952.5

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