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- PDB-2qsr: Crystal structure of C-terminal domain of transcription-repair co... -

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Basic information

Entry
Database: PDB / ID: 2qsr
TitleCrystal structure of C-terminal domain of transcription-repair coupling factor
ComponentsTranscription-repair coupling factor
KeywordsTRANSCRIPTION / structural genomics / Transcription-repair / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-binding / Helicase / Hydrolase / Nucleotide-binding
Function / homology
Function and homology information


transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / DNA translocase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Transcription-repair-coupling factor, D7 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 ...Transcription-repair-coupling factor, D7 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 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Transcription-repair-coupling factor
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsRamagopal, U.A. / Toro, R. / Gilmore, M. / Bain, K. / Iizuka, M. / Wasserman, S. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of C-terminal domain of transcription-repair coupling factor.
Authors: Ramagopal, U.A. / Toro, R. / Gilmore, M. / Bain, K. / Iizuka, M. / Wasserman, S. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription-repair coupling factor


Theoretical massNumber of molelcules
Total (without water)20,5061
Polymers20,5061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.891, 84.891, 122.021
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Transcription-repair coupling factor


Mass: 20506.107 Da / Num. of mol.: 1 / Fragment: C-terminal domain: Residues 1007-1168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: mfd, spr0006 / Plasmid: BS-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DRQ1

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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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Sodium citrate pH 6.5, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 19.4 % / Av σ(I) over netI: 4.6 / Number: 99779 / Rmerge(I) obs: 0.127 / Χ2: 0.72 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 5156 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.675099.810.0531.25816.5
5.36.6710010.0860.67219.4
4.635.310010.0830.6619.8
4.214.6310010.1190.93520.2
3.914.2110010.1330.62820.4
3.683.9110010.2080.80320
3.493.6810010.280.66419.8
3.343.4910010.4290.53919.5
3.213.3499.810.5790.51819.3
3.13.2110010.8170.48419.1
ReflectionResolution: 3.1→50 Å / Num. all: 5156 / Num. obs: 5156 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Rmerge(I) obs: 0.127 / Χ2: 0.718 / Net I/σ(I): 4.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 3.24 / Num. unique all: 493 / Rsym value: 0.707 / Χ2: 0.484 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RESOLVEphasing
RefinementResolution: 3.1→42.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 40.316 / SU ML: 0.31 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 234 4.6 %RANDOM
Rwork0.184 ---
all0.187 5117 --
obs0.187 5117 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å20 Å2
2---0.45 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 3.1→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 0 0 1329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221347
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9881810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1625.14768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02215272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.06158
X-RAY DIFFRACTIONr_chiral_restr0.080.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02987
X-RAY DIFFRACTIONr_nbd_refined0.2750.3672
X-RAY DIFFRACTIONr_nbtor_refined0.3510.5950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.596
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3510.55
X-RAY DIFFRACTIONr_mcbond_it5.2232805
X-RAY DIFFRACTIONr_mcangle_it7.77331294
X-RAY DIFFRACTIONr_scbond_it6.6562582
X-RAY DIFFRACTIONr_scangle_it10.023516
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 21 -
Rwork0.249 336 -
all-357 -
obs--100 %
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)
15.5799-0.63683.19463.41971.15776.99470.07040.8955-0.1743-0.05050.1526-0.35970.52090.874-0.22310.20280.0772-0.0257-0.0888-0.01930.260333.0544.10259.177
22.5873.07341.96518.33255.11679.2302-0.37240.7213-0.3737-0.48040.6972-0.63310.42761.1933-0.3248-0.01760.05380.02160.2068-0.09840.232333.82641.70945.863
35.70411.63912.18465.54261.24485.75960.1311-0.19360.1160.2966-0.06040.0378-0.2704-0.2391-0.0707-0.07810.0336-0.0134-0.09140.01810.192328.36956.44463.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1005 - 10192 - 16
2X-RAY DIFFRACTION2AA1020 - 108217 - 79
3X-RAY DIFFRACTION3AA1083 - 116580 - 162

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