- PDB-3vir: Crystal strcture of Swi5 from fission yeast -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3vir
Title
Crystal strcture of Swi5 from fission yeast
Components
Mating-type switching protein swi5
Keywords
RECOMBINATION ACTIVATOR / Sfr1
Function / homology
Function and homology information
meiotic strand invasion / meiotic DNA recombinase assembly involved in reciprocal meiotic recombination / Swi5-Sfr1 complex / Swi5-Swi2 complex / meiotic joint molecule formation / gene conversion at mating-type locus / mating type switching / DNA recombinase assembly / DNA strand invasion / ATPase activator activity ...meiotic strand invasion / meiotic DNA recombinase assembly involved in reciprocal meiotic recombination / Swi5-Sfr1 complex / Swi5-Swi2 complex / meiotic joint molecule formation / gene conversion at mating-type locus / mating type switching / DNA recombinase assembly / DNA strand invasion / ATPase activator activity / double-strand break repair via homologous recombination / DNA recombination / identical protein binding Similarity search - Function
DNA repair protein, Swi5 / Swi5 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.5 / % possible all: 62.1
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Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
SOLVE
phasing
REFMAC
5.6.0113
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MIR / Resolution: 2.7→19.65 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.875 / SU B: 25.977 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3106
776
5 %
RANDOM
Rwork
0.25087
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-
-
all
0.25378
17174
-
-
obs
0.25378
14795
86.15 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 65.085 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.43 Å2
0 Å2
-0.43 Å2
2-
-
3.11 Å2
0 Å2
3-
-
-
-0.78 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→19.65 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1950
0
40
0
1990
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
2006
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
1355
X-RAY DIFFRACTION
r_angle_refined_deg
1.754
1.976
2687
X-RAY DIFFRACTION
r_angle_other_deg
1.02
3
3353
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.147
5
247
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.203
25.652
92
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
22.583
15
390
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.155
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
322
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2157
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
341
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.7→2.769 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.526
36
-
Rwork
0.357
692
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obs
-
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58.1 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
19.6361
-4.1522
-7.6367
1.4669
1.4857
3.2109
0.2341
-0.3973
0.0296
0.0945
-0.1508
-0.0923
-0.1492
0.2386
-0.0833
0.1024
0.0499
-0.05
0.4962
-0.0322
0.0759
15.2888
15.4505
20.3677
2
27.3928
-7.786
-8.9481
2.8736
2.7254
3.6244
0.8339
0.1116
0.2216
-0.3292
-0.4408
-0.1291
-0.3444
-0.0193
-0.3931
0.0632
0.0636
0.0241
0.4594
0.0194
0.1601
12.0368
17.7509
9.629
3
9.098
-1.3209
2.6088
1.6137
-0.1447
1.0022
-0.1742
-0.1614
0.0087
0.169
0.1636
0.1982
-0.0091
-0.1074
0.0106
0.0294
0.0368
0.0091
0.5279
0.0008
0.0386
59.0438
-8.0826
17.5512
4
15.9811
-5.634
5.0034
2.9402
-1.7001
1.6215
0.2626
0.3321
0.1298
-0.2476
-0.2276
-0.058
0.1256
0.1484
-0.0351
0.0787
0.0727
-0.0602
0.5229
-0.0139
0.089
64.9133
-9.9262
7.2958
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
11 - 79
2
X-RAY DIFFRACTION
2
B
2 - 67
3
X-RAY DIFFRACTION
3
C
14 - 66
4
X-RAY DIFFRACTION
4
D
10 - 72
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