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- PDB-3bzj: UVDE K229L -

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Basic information

Entry
Database: PDB / ID: 3bzj
TitleUVDE K229L
ComponentsUV endonuclease
KeywordsHYDROLASE / UVDE / endonuclease / DNA repair / TIM barrel / 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: 2.3 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 18, 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_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
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

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Assembly

Deposited unit
A: UV endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4076
Polymers33,9681
Non-polymers4395
Water1,76598
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)68,81412
Polymers67,9352
Non-polymers87810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area2640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.390, 113.390, 89.390
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 / UVDE K229L


Mass: 33967.629 Da / Num. of mol.: 1 / Mutation: K229L
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Ammoniumsulfate, Acetate, Lithiumsulfate, pH6.0, 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: 2.3→37.1 Å / Num. all: 15564 / Num. obs: 15387 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 21.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.367 / % 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 2J6V

2j6v


Resolution: 2.3→34.28 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.413 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.303 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24414 772 5 %RANDOM
Rwork0.18765 ---
all0.19042 14615 --
obs0.19042 14615 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.717 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 21 98 2387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212341
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9873186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8355291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86422.605119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84115391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441529
X-RAY DIFFRACTIONr_chiral_restr0.1040.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021840
X-RAY DIFFRACTIONr_nbd_refined0.1980.2999
X-RAY DIFFRACTIONr_nbtor_refined0.30.21534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.27
X-RAY DIFFRACTIONr_mcbond_it0.7591.51471
X-RAY DIFFRACTIONr_mcangle_it1.22822280
X-RAY DIFFRACTIONr_scbond_it1.9683974
X-RAY DIFFRACTIONr_scangle_it3.0554.5906
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 65 -
Rwork0.198 1046 -
obs--99.64 %

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