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- PDB-1okb: crystal structure of Uracil-DNA glycosylase from Atlantic cod (Ga... -

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Basic information

Entry
Database: PDB / ID: 1okb
Titlecrystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE / URACIL-DNA GLYCOSYLASE / COLD-ADAPTATION / BASE EXCISION REPAIR / STRUCTURE-FUNCTION RELATIONSHIP
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / mitochondrion / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesGADUS MORHUA (Atlantic cod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeiros, I. / Moe, E. / Lanes, O. / Smalas, A.O. / Willassen, N.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The Crystal Structure of Uracil-DNA Glycosylase from Atlantic Cod (Gadus Morhua) Reveals Cold-Adaptation Features
Authors: Leiros, I. / Moe, E. / Lanes, O. / Smalas, A.O. / Willassen, N.P.
History
DepositionJul 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
B: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8316
Polymers50,5762
Non-polymers2554
Water6,179343
1
A: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4153
Polymers25,2881
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4153
Polymers25,2881
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.580, 67.189, 68.644
Angle α, β, γ (deg.)90.00, 119.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.49805, 5.0E-5, 0.86715), (-0.00015, -1, -2.0E-5), (0.86715, -0.00014, 0.49805)
Vector: 17.1628, 29.41696, 29.79831)

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Components

#1: Protein URACIL-DNA GLYCOSYLASE


Mass: 25287.910 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 79-301 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GADUS MORHUA (Atlantic cod) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I983, uridine nucleosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES PRO 82 MET, ALA 83 GLU, GLY 84 PHE
Sequence detailsTHE THREE N-TERMINAL RESIDUES M82, E83, F84 ARE ENCODED BY THE EXPRESSION VECTOR.

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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: 2.71 Å3/Da / Density % sol: 54.7 %
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 1.4M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→12 Å / Num. obs: 42162 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 19.45 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKZ

1akz


Resolution: 1.9→12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 2112 4.9 %RANDOM
Rwork0.1861 ---
obs0.1861 42162 98.7 %-
Displacement parametersBiso mean: 22.4043 Å2
Baniso -1Baniso -2Baniso -3
1-1.623 Å20 Å22.017 Å2
2---3.129 Å20 Å2
3---1.506 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 14 343 3931
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.189
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.207
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.832
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2911.5
X-RAY DIFFRACTIONc_mcangle_it2.0032
X-RAY DIFFRACTIONc_scbond_it2.1252
X-RAY DIFFRACTIONc_scangle_it3.1842.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.0207 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2801 182 4.26 %
Rwork0.2586 3955 -
obs--96.88 %

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