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- PDB-2nrt: Crystal structure of the C-terminal half of UvrC -

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Basic information

Entry
Database: PDB / ID: 2nrt
TitleCrystal structure of the C-terminal half of UvrC
ComponentsUvrABC system protein C
KeywordsHYDROLASE / UvrC / endonuclease / RNAse H / helix hairpin helix / NER / UvrABC
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: 1.5 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5646
Polymers25,3861
Non-polymers1775
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.375, 72.782, 91.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25386.404 Da / Num. of mol.: 1
Fragment: RNAse H endonuclease 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 (DE3)-RIL / References: UniProt: Q9WYA3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 0.1 M HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.009
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 37576 / Num. obs: 37576 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.13 / Net I/σ(I): 14
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.417 / Num. unique all: 3672 / Χ2: 1.092 / % possible all: 97.6

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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: 1.5→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.865 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1902 5.1 %RANDOM
Rwork0.185 ---
all0.187 37519 --
obs0.187 37519 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 5 206 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221794
X-RAY DIFFRACTIONr_bond_other_d0.0010.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.982415
X-RAY DIFFRACTIONr_angle_other_deg0.86633955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21522.87487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6791519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined0.220.2379
X-RAY DIFFRACTIONr_nbd_other0.1960.21706
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2865
X-RAY DIFFRACTIONr_nbtor_other0.0870.21074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.217
X-RAY DIFFRACTIONr_mcbond_it1.8881.51167
X-RAY DIFFRACTIONr_mcbond_other0.6581.5440
X-RAY DIFFRACTIONr_mcangle_it2.55221754
X-RAY DIFFRACTIONr_scbond_it3.2313757
X-RAY DIFFRACTIONr_scangle_it4.554.5661
X-RAY DIFFRACTIONr_rigid_bond_restr1.69433812
X-RAY DIFFRACTIONr_sphericity_free8.4893211
X-RAY DIFFRACTIONr_sphericity_bonded3.00233465
LS refinement shellResolution: 1.502→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 113 -
Rwork0.179 2252 -
obs-2365 83.69 %

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