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- PDB-7egt: The crystal structure of the C-terminal domain of T. thermophilus... -

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Basic information

Entry
Database: PDB / ID: 7egt
TitleThe crystal structure of the C-terminal domain of T. thermophilus UvrD complexed with the N-terminal domain of UvrB
Components
  • DNA helicase UvrD
  • UvrABC system protein B
KeywordsTRANSCRIPTION / TCR / Thermus thermophilus / RNA polymerase / UvrD / UvrB / DNA repair
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / DNA 3'-5' helicase / isomerase activity / DNA helicase activity / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal ...UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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
Similarity search - Domain/homology
DNA 3'-5' helicase / UvrABC system protein B
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.581 Å
AuthorsZheng, F. / Shen, L. / Li, L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670067 China
CitationJournal: Nature / Year: 2022
Title: Crucial role and mechanism of transcription-coupled DNA repair in bacteria.
Authors: Bharati, B.K. / Gowder, M. / Zheng, F. / Alzoubi, K. / Svetlov, V. / Kamarthapu, V. / Weaver, J.W. / Epshtein, V. / Vasilyev, N. / Shen, L. / Zhang, Y. / Nudler, E.
History
DepositionMar 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UvrABC system protein B
B: DNA helicase UvrD
C: UvrABC system protein B
D: DNA helicase UvrD


Theoretical massNumber of molelcules
Total (without water)107,1924
Polymers107,1924
Non-polymers00
Water1,13563
1
A: UvrABC system protein B
D: DNA helicase UvrD


Theoretical massNumber of molelcules
Total (without water)53,5962
Polymers53,5962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA helicase UvrD
C: UvrABC system protein B


Theoretical massNumber of molelcules
Total (without water)53,5962
Polymers53,5962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.332, 114.606, 125.448
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UvrABC system protein B / Protein UvrB / Excinuclease ABC subunit B


Mass: 47175.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: uvrB, TTHA1892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56243
#2: Protein DNA helicase UvrD


Mass: 6420.366 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: uvrD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O24736, DNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 41725 / % possible obs: 98.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Χ2: 1.193 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.644.80.99218830.7040.4761.1060.92790.9
2.64-2.695.10.86719820.8210.4050.9610.96894.7
2.69-2.745.40.79320120.8010.3640.8770.96195.9
2.74-2.85.60.74920290.8320.340.8260.98597.2
2.8-2.865.80.68720200.8830.3090.7550.98898
2.86-2.9360.64320430.890.2850.7050.98898.2
2.93-36.10.57220850.9050.2530.6271.02398.6
3-3.085.90.4620800.9420.2070.5061.07699.7
3.08-3.175.90.39920710.9440.1810.4391.10899.6
3.17-3.286.60.32320920.9760.1380.3521.164100
3.28-3.396.70.2721060.980.1130.2931.191100
3.39-3.536.70.20720850.9880.0870.2251.28899.6
3.53-3.696.70.16621220.9910.070.181.345100
3.69-3.886.60.13221190.9920.0560.1431.433100
3.88-4.1360.10321180.9940.0450.1131.506100
4.13-4.456.60.08621190.9950.0370.0941.502100
4.45-4.896.80.07121410.9970.030.0781.484100
4.89-5.66.50.06421460.9960.0270.071.234100
5.6-7.056.10.05821790.9980.0250.0641.16399.9
7.05-5060.03922930.9990.0170.0421.14399.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D2M

1d2m


Resolution: 2.581→46.166 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1992 4.8 %
Rwork0.2149 39525 -
obs0.2166 41517 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.88 Å2 / Biso mean: 62.5845 Å2 / Biso min: 36.38 Å2
Refinement stepCycle: final / Resolution: 2.581→46.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7234 0 0 63 7297
Biso mean---60.61 -
Num. residues----912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.581-2.64520.33891190.3347235282
2.6452-2.71670.33621360.3142271095
2.7167-2.79660.33671400.3115277297
2.7966-2.88690.34841400.2975281098
2.8869-2.99010.37261410.2855278398
2.9901-3.10970.34271420.2684283399
3.1097-3.25120.31471450.25762864100
3.2512-3.42260.25121440.2512873100
3.4226-3.6370.26451450.21252858100
3.637-3.91760.25621450.19932884100
3.9176-4.31160.21481470.18252904100
4.3116-4.93490.18641480.17472915100
4.9349-6.21510.27311490.20692948100
6.2151-460.17911510.1729301998

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