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- PDB-1yd3: Crystal structure of the GIY-YIG N-terminal endonuclease domain o... -

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Basic information

Entry
Database: PDB / ID: 1yd3
TitleCrystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y43F bound to its catalytic divalent cation
ComponentsUvrABC system protein C
KeywordsDNA BINDING PROTEIN
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
GIY-YIG endonuclease / 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 endonuclease / GIY-YIG type nucleases (URI domain) ...GIY-YIG endonuclease / 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 endonuclease / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / UvrABC system protein C
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsTruglio, J.J. / Rhau, B. / Croteau, D.L. / Wang, L. / Skorvaga, M. / Karakas, E. / DellaVecchia, M.J. / Wang, H. / Van Houten, B. / Kisker, C.
CitationJournal: Embo J. / Year: 2005
Title: Structural insights into the first incision reaction during nucleotide excision repair
Authors: Truglio, J.J. / Rhau, B. / Croteau, D.L. / Wang, L. / Skorvaga, M. / Karakas, E. / Dellavecchia, M.J. / Wang, H. / Van Houten, B. / Kisker, C.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UvrABC system protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7297
Polymers11,3621
Non-polymers3676
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.094, 56.094, 111.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2129-

HOH

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Components

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


Mass: 11362.382 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: Y43F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYA3
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#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.: 173 / 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: 3.7 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.1
SYNCHROTRONNSLS X12B21.1
SYNCHROTRONNSLS X2531.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 44684 / Num. obs: 44684 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.052 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.072 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19381 1220 5.1 %RANDOM
Rwork0.17457 ---
all0.18 22868 --
obs0.1755 22868 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 11 173 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022765
X-RAY DIFFRACTIONr_bond_other_d0.0010.02751
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.0081021
X-RAY DIFFRACTIONr_angle_other_deg0.91331752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.233589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.53223.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14815161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.583158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02152
X-RAY DIFFRACTIONr_nbd_refined0.2160.2101
X-RAY DIFFRACTIONr_nbd_other0.1540.2567
X-RAY DIFFRACTIONr_nbtor_refined0.1560.2336
X-RAY DIFFRACTIONr_nbtor_other0.070.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.219
X-RAY DIFFRACTIONr_mcbond_it1.7681.5605
X-RAY DIFFRACTIONr_mcbond_other0.5151.5181
X-RAY DIFFRACTIONr_mcangle_it1.92732
X-RAY DIFFRACTIONr_scbond_it3.1763368
X-RAY DIFFRACTIONr_scangle_it4.2274.5289
X-RAY DIFFRACTIONr_rigid_bond_restr3.43531814
X-RAY DIFFRACTIONr_sphericity_free5.5733178
X-RAY DIFFRACTIONr_sphericity_bonded2.72331505
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 98 -
Rwork0.176 1575 -
obs--96.99 %

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