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- PDB-4gle: SacUVDE in complex with 6-4PP-containing DNA -

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Basic information

Entry
Database: PDB / ID: 4gle
TitleSacUVDE in complex with 6-4PP-containing DNA
Components
  • 5'-D(*CP*GP*TP*CP*GP*TP*CP*AP*AP*GP*GP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*TP*CP*CP*(64T)P*(5PY)P*GP*AP*CP*GP*AP*CP*G)-3'
  • UV damage endonuclease
KeywordsHYDROLASE/DNA / TIM barrel / HYDROLASE-DNA complex
Function / homology
Function and homology information


Hydrolases / 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
DNA / DNA (> 10) / UV damage endonuclease
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeulenbroek, E.M. / Peron Cane, C. / Jala, I. / Iwai, S. / Moolenaar, G.F. / Goosen, N. / Pannu, N.S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions.
Authors: Meulenbroek, E.M. / Peron Cane, C. / Jala, I. / Iwai, S. / Moolenaar, G.F. / Goosen, N. / Pannu, N.S.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*CP*GP*TP*CP*GP*TP*CP*AP*AP*GP*GP*AP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*TP*CP*CP*(64T)P*(5PY)P*GP*AP*CP*GP*AP*CP*G)-3'
A: UV damage endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0745
Polymers44,8823
Non-polymers1922
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-43 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 112.510, 153.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*CP*GP*TP*CP*GP*TP*CP*AP*AP*GP*GP*AP*CP*GP*C)-3'


Mass: 4594.986 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*GP*TP*CP*CP*(64T)P*(5PY)P*GP*AP*CP*GP*AP*CP*G)-3'


Mass: 4587.989 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein UV damage endonuclease


Mass: 35698.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: uvdE, Saci_1096 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9T1, Hydrolases
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG2000 MME, 100 mM acetate buffer, pH 4.6, 200 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2012
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→52.834 Å / Num. all: 14055 / Num. obs: 14041 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0024refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TC3

3tc3


Resolution: 2.7→52.834 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.216 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.763 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26184 698 5 %RANDOM
Rwork0.19139 ---
all0.19475 13316 --
obs0.19475 13316 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.704 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å2-0 Å20 Å2
2---1.3 Å2-0 Å2
3---4.5 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 609 10 4 2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0173086
X-RAY DIFFRACTIONr_bond_other_d0.0060.022694
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.7944287
X-RAY DIFFRACTIONr_angle_other_deg1.2713.0016231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1895291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24424.464112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81115469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7671516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 44 -
Rwork0.327 945 -
obs--98.21 %

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