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- PDB-3hjh: A rigid N-terminal clamp restrains the motor domains of the bacte... -

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Basic information

Entry
Database: PDB / ID: 3hjh
TitleA rigid N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor
ComponentsTranscription-repair-coupling factor
KeywordsHYDROLASE / MFD / MUTATION FREQUENCY DECLINE / TRANSCRIPTION-COUPLED DNA REPAIR / TRANSCRIPTION-REPAIR COUPLING FACTOR / ATP-binding / DNA damage / DNA repair / DNA-binding / Helicase / Nucleotide-binding
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 - #11140 / 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 ...Rossmann fold - #11140 / 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
: / Transcription-repair-coupling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMurphy, M. / Gong, P. / Ralto, K. / Manelyte, L. / Savery, N. / Theis, K.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd.
Authors: Murphy, M.N. / Gong, P. / Ralto, K. / Manelyte, L. / Savery, N.J. / Theis, K.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,1472
Polymers55,0891
Non-polymers591
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.062, 157.650, 35.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transcription-repair-coupling factor / TRCF / ATP-dependent helicase mfd


Mass: 55088.551 Da / Num. of mol.: 1 / Fragment: UNP residues 1-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1114, JW1100, mfd / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30958, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8% PEG 4000, 0.01 M CO(II)CL2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2006 / Details: doubly focusing toroidal mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.93→79.06 Å / Num. obs: 36838 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 27.9
Reflection shellResolution: 1.93→1.99 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EYQ

2eyq


Resolution: 1.95→42.03 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.7 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25731 1788 5 %RANDOM
Rwork0.21047 ---
obs0.21282 34090 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.156 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2---2.07 Å20 Å2
3---3.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 1 318 3888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213652
X-RAY DIFFRACTIONr_bond_other_d0.0020.023356
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9654961
X-RAY DIFFRACTIONr_angle_other_deg0.79437786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024065
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02751
X-RAY DIFFRACTIONr_nbd_refined0.1910.2819
X-RAY DIFFRACTIONr_nbd_other0.2260.23984
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.14422236
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.84933613
X-RAY DIFFRACTIONr_scbond_it3.37821416
X-RAY DIFFRACTIONr_scangle_it4.45731348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 128
Rwork0.28 2503
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22370.65660.15052.03050.33990.512-0.04490.00360.03640.03730.02730.10580.01850.02070.01750.26750.0010.01990.2928-0.00260.001568.25649.49815.534
22.2034-0.36020.97021.7782-0.06442.70930.09990.0726-0.052-0.21210.04980.0689-0.0431-0.2195-0.14970.3574-0.02790.02080.36380.00650.213345.10743.728-3.197
32.6793-0.1128-0.02361.4120.38221.1275-0.0559-0.01110.01470.0589-0.03580.5735-0.1403-0.25920.09170.41830.03010.04450.36740.01860.44757.0283.91324.066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 126
2X-RAY DIFFRACTION1A216 - 353
3X-RAY DIFFRACTION2A127 - 215
4X-RAY DIFFRACTION3A354 - 450

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