RNA exonuclease activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA biosynthetic process / nucleotidyltransferase activity / DNA recombination / DNA-directed DNA polymerase activity / DNA repair / DNA binding / ATP binding / metal ion binding Similarity search - Function
DNA ligase D / LigD polymerase domain, PaeLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. ...DNA ligase D / LigD polymerase domain, PaeLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / YTTRIUM (III) ION / Multifunctional non-homologous end joining protein LigD Similarity search - Component
Biological species
Pseudomonas aeruginosa (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.92 Å
Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG ...Details: Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG 5000 monomethylether (MME) (20 - 30%), 100 mM 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.8 - 7.0, 200 mM ammonium sulfate, and 10 mM yttrium (III) chloride at 22 C. , VAPOR DIFFUSION, SITTING DROP, temperature 298K
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
130
1
2
1
3
1
Diffraction source
Source
Site
Beamline
Type
ID
Wavelength (Å)
SYNCHROTRON
NSLS
X12C
1
1.190.990.73
SYNCHROTRON
NSLS
X25
2
1.190.990.73
ROTATING ANODE
RIGAKU RU300
3
1.54
Detector
Type
ID
Detector
Date
Details
ADSC QUANTUM 315
1
CCD
Feb 20, 2010
SeeNSLSX25BeamlineDescription
ADSC QUANTUM 210
2
CCD
Feb 20, 2010
SeeNSLSX12CBeamlineDescription
RIGAKU RAXIS IV++
3
IMAGE PLATE
Feb 10, 2010
Osmicconfocalmirrors
Radiation
Monochromator: See Beamline Documentation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.19
1
2
0.99
1
3
0.73
1
4
1.54
1
Reflection
Resolution: 1.92→50 Å / Num. all: 25728 / Num. obs: 24596 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.087 / Net I/σ(I): 25.9
Reflection shell
Resolution: 1.92→1.95 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 1272 / % possible all: 93
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SOLVE
phasing
PHENIX
(phenix.refine: 1.6_289)
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MIR / Resolution: 1.92→37.395 Å / SU ML: 0.2 / σ(F): 0.06 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1988
2387
9.95 %
10% selected at random in CCP4/Unique
Rwork
0.1475
-
-
-
obs
0.1527
23992
92.95 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.778 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
5.3212 Å2
-1.2709 Å2
-1.1842 Å2
2-
-
-1.6351 Å2
0.4754 Å2
3-
-
-
-3.7302 Å2
Refinement step
Cycle: LAST / Resolution: 1.92→37.395 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2439
0
34
358
2831
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
2617
X-RAY DIFFRACTION
f_angle_d
1.249
3556
X-RAY DIFFRACTION
f_dihedral_angle_d
14.969
993
X-RAY DIFFRACTION
f_chiral_restr
0.1
370
X-RAY DIFFRACTION
f_plane_restr
0.005
463
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.92-1.9886
0.2438
208
0.1666
1912
X-RAY DIFFRACTION
82
1.9886-2.0682
0.2206
241
0.1376
2149
X-RAY DIFFRACTION
92
2.0682-2.1624
0.2045
239
0.1386
2170
X-RAY DIFFRACTION
94
2.1624-2.2763
0.2545
200
0.1725
1597
X-RAY DIFFRACTION
70
2.2763-2.4189
0.2095
244
0.162
2195
X-RAY DIFFRACTION
94
2.4189-2.6057
0.2057
263
0.1515
2272
X-RAY DIFFRACTION
99
2.6057-2.8678
0.2094
223
0.1598
2353
X-RAY DIFFRACTION
100
2.8678-3.2826
0.1962
247
0.1507
2340
X-RAY DIFFRACTION
100
3.2826-4.1348
0.1807
254
0.1239
2325
X-RAY DIFFRACTION
99
4.1348-37.4023
0.1645
268
0.1364
2292
X-RAY DIFFRACTION
100
+
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