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- PDB-1yd6: Crystal structure of the GIY-YIG N-terminal endonuclease domain o... -

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Basic information

Entry
Database: PDB / ID: 1yd6
TitleCrystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus caldotenax
ComponentsUvrCUvrABC endonuclease
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / 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 ...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 catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / 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 speciesBacillus caldotenax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: UvrC
B: UvrC
C: UvrC
D: UvrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28010
Polymers45,8854
Non-polymers3956
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-96 kcal/mol
Surface area20230 Å2
MethodPISA
2
A: UvrC
B: UvrC
C: UvrC
D: UvrC
hetero molecules

A: UvrC
B: UvrC
C: UvrC
D: UvrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55920
Polymers91,7708
Non-polymers78912
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10980 Å2
ΔGint-182 kcal/mol
Surface area37260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.487, 86.660, 67.862
Angle α, β, γ (deg.)90.00, 120.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1042-

HOH

21D-121-

HOH

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Components

#1: Protein
UvrC / UvrABC endonuclease


Mass: 11471.286 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldotenax (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KWH6*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Ammonium Sulfate, DTT, Sodium Acetate, pH 5.4, 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
SYNCHROTRONNSLS X12B21
SYNCHROTRONNSLS X2531
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 29029 / Num. obs: 29029 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.08 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.209 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.186 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25203 1487 5.1 %RANDOM
Rwork0.2024 ---
all0.219 27724 --
obs0.20496 27724 100 %-
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: 36.111 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-2.24 Å2
2--0.83 Å20 Å2
3----2.65 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 18 126 3110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223026
X-RAY DIFFRACTIONr_bond_other_d0.0010.022797
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9914068
X-RAY DIFFRACTIONr_angle_other_deg0.86936547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15424.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87515594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.41513
X-RAY DIFFRACTIONr_chiral_restr0.1070.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined0.2120.2630
X-RAY DIFFRACTIONr_nbd_other0.1830.22632
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21455
X-RAY DIFFRACTIONr_nbtor_other0.0890.21706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.215
X-RAY DIFFRACTIONr_mcbond_it1.0621.51932
X-RAY DIFFRACTIONr_mcbond_other0.211.5762
X-RAY DIFFRACTIONr_mcangle_it1.67522985
X-RAY DIFFRACTIONr_scbond_it2.30331260
X-RAY DIFFRACTIONr_scangle_it3.3834.51083
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 101 -
Rwork0.209 2013 -
obs--100 %

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