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- PDB-2nrx: Crystal structure of the C-terminal half of UvrC, in the presence... -

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Basic information

Entry
Database: PDB / ID: 2nrx
TitleCrystal structure of the C-terminal half of UvrC, in the presence of sulfate molecules
ComponentsUvrABC system protein C
KeywordsHYDROLASE / uvrC / RNAse H / endonuclase / helix hairpin helix / UvrABC / NER
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / DNA damage response / DNA binding / cytoplasm
Similarity search - Function
UvrC, RNAse H endonuclease domain / UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / : / : / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease ...UvrC, RNAse H endonuclease domain / UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / : / : / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG endonuclease superfamily / GIY-YIG catalytic domain / GIY-YIG domain profile. / UVR domain superfamily / UvrB/uvrC motif / UVR domain / UVR domain profile. / RuvA domain 2-like / Helix-hairpin-helix domain / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UvrABC system protein C
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKarakas, E. / Truglio, J.J. / Kisker, C.
CitationJournal: Embo J. / Year: 2007
Title: Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.
Authors: Karakas, E. / Truglio, J.J. / Croteau, D. / Rhau, B. / Wang, L. / Van Houten, B. / Kisker, C.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 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 1.4Aug 30, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: UvrABC system protein C
B: UvrABC system protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,63311
Polymers50,7732
Non-polymers8619
Water6,017334
1
A: UvrABC system protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8636
Polymers25,3861
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UvrABC system protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7715
Polymers25,3861
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.359, 81.015, 99.619
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UvrABC system protein C / Protein uvrC / Excinuclease ABC subunit C


Mass: 25386.404 Da / Num. of mol.: 2
Fragment: The RNAse H endonuclase and helix hairpin helix domains (residues 339-557)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: uvrC / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (CE3)-RIL / References: UniProt: Q9WYA3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium sulfate, 0.05 M Tris (pH 8.5), 0.025 M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 42886 / Num. obs: 42886 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Χ2: 1.141 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.337 / Num. unique all: 4220 / Χ2: 1.081 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NRR

2nrr


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.972 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2145 5 %RANDOM
Rwork0.184 ---
all0.187 40886 --
obs0.187 40886 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.321 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20.12 Å2
2--2.29 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 46 334 3826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223545
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9934774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37722.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35615668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1231538
X-RAY DIFFRACTIONr_chiral_restr0.1380.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022616
X-RAY DIFFRACTIONr_nbd_refined0.2240.21720
X-RAY DIFFRACTIONr_nbtor_refined0.310.22382
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.225
X-RAY DIFFRACTIONr_mcbond_it1.0221.52200
X-RAY DIFFRACTIONr_mcangle_it1.59223429
X-RAY DIFFRACTIONr_scbond_it2.68431491
X-RAY DIFFRACTIONr_scangle_it4.2114.51345
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 144 -
Rwork0.201 2937 -
obs-3081 95.33 %
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)
12.5164-0.2678-1.43830.66590.49533.88050.07050.1489-0.0863-0.05460.01960.037-0.0002-0.1942-0.0901-0.06440.0043-0.0171-0.10.0052-0.059611.4780.403918.9955
23.99472.7932-1.55644.7499-0.57135.6945-0.18560.36420.0794-0.00430.2080.2920.3087-0.3298-0.0225-0.0607-0.00080.0249-0.06360.0704-0.081934.556929.07885.1153
33.34170.0979-0.64561.4889-0.93232.1257-0.017-0.4367-0.3202-0.0265-0.01060.020.0780.18720.0276-0.10150.0008-0.01880.01220.1046-0.069711.3663-11.860650.0235
46.95720.77932.55532.47840.35746.9053-0.13610.4954-0.0139-0.2950.24990.08120.0602-0.2134-0.1138-0.0027-0.04810.0054-0.0022-0.0026-0.16887.3207-10.235677.7121
50.21180.0809-0.10370.1947-0.2530.32860.0396-0.0263-0.0219-0.00550.02940.0305-0.0277-0.0032-0.069-0.02420.00380.0077-0.03170.0263-0.013814.03350.945434.9154
60.11560.1182-0.24890.5493-0.99711.8230.15710.0087-0.15170.1837-0.1464-0.0065-0.25180.1906-0.0107-0.0016-0.026-0.022-0.00860.02410.015514.5934-3.621335.2952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A341 - 494
2X-RAY DIFFRACTION2A495 - 557
3X-RAY DIFFRACTION3B342 - 494
4X-RAY DIFFRACTION4B495 - 557
5X-RAY DIFFRACTION5A3 - 334
6X-RAY DIFFRACTION5B1 - 333
7X-RAY DIFFRACTION6A901 - 904
8X-RAY DIFFRACTION6B901 - 904

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