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- PDB-3c0l: UVDE K229R -

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Basic information

Entry
Database: PDB / ID: 3c0l
TitleUVDE K229R
ComponentsUV endonuclease
KeywordsHYDROLASE / UVDE / TIM barrel / endonuclease / DNA repair / Plasmid
Function / homology
Function and homology information


response to UV / nucleotide-excision repair / endonuclease activity / metal ion binding
Similarity search - Function
UV-endonuclease UvdE / UV-endonuclease UvdE / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Probable UV endonuclease
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsMeulenbroek, E.M. / Paspaleva, K. / Thomassen, E.A.J. / Abrahams, J.P. / Goosen, N. / Pannu, N.S.
CitationJournal: Protein Sci. / Year: 2009
Title: Involvement of a carboxylated lysine in UV damage endonuclease
Authors: Meulenbroek, E.M. / Paspaleva, K. / Thomassen, E.A. / Abrahams, J.P. / Goosen, N. / Pannu, N.S.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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: UV endonuclease


Theoretical massNumber of molelcules
Total (without water)34,0121
Polymers34,0121
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UV endonuclease

A: UV endonuclease


Theoretical massNumber of molelcules
Total (without water)68,0232
Polymers68,0232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.110, 107.110, 91.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UV endonuclease


Mass: 34011.664 Da / Num. of mol.: 1 / Mutation: L133I, K229R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q746K1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Acetate, pH5.6, 1M Naformate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MAR225 / Detector: CCD / Date: Jul 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.15→46.18 Å / Num. all: 5706 / Num. obs: 5367 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 18.3
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 11 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 6.6 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BESTdata collection
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BZG

3bzg


Resolution: 3.15→46.18 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.855 / SU B: 20.921 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 245 4.6 %RANDOM
Rwork0.19463 ---
all0.19703 5122 --
obs0.19703 5122 94.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.563 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.15→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 0 2 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212252
X-RAY DIFFRACTIONr_angle_refined_deg0.9451.9783051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1122.212113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1081529
X-RAY DIFFRACTIONr_chiral_restr0.0620.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021752
X-RAY DIFFRACTIONr_nbd_refined0.1830.2909
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.23
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 19 -
Rwork0.232 363 -
obs--95.74 %

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