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- PDB-3c0q: UVDE E175A -

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Basic information

Entry
Database: PDB / ID: 3c0q
TitleUVDE E175A
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: 2.74 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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UV endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2164
Polymers33,9691
Non-polymers2473
Water48627
1


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

A: UV endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4318
Polymers67,9372
Non-polymers4946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area2040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.380, 113.380, 89.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-281-

SO4

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Components

#1: Protein UV endonuclease


Mass: 33968.617 Da / Num. of mol.: 1 / Mutation: E175A
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.5M ammonium sulfate, 0.1M acetate, pH6.0, 1M lithium sulfate, 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: 2.74→35.03 Å / Num. all: 9336 / Num. obs: 9213 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 8
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.364 / % possible all: 99.8

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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: 2.74→35.03 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / SU B: 26.636 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 440 4.8 %RANDOM
Rwork0.19816 ---
all0.20034 8773 --
obs0.20034 8773 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.74→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 11 27 2269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212294
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9813115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24222.435115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63115382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8941528
X-RAY DIFFRACTIONr_chiral_restr0.0930.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021790
X-RAY DIFFRACTIONr_nbd_refined0.2020.2995
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.23
X-RAY DIFFRACTIONr_mcbond_it0.4061.51431
X-RAY DIFFRACTIONr_mcangle_it0.70822227
X-RAY DIFFRACTIONr_scbond_it0.9733965
X-RAY DIFFRACTIONr_scangle_it1.6684.5888
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 31 -
Rwork0.295 636 -
obs--99.7 %

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