Journal: J Mol Biol / Year: 2007 Title: Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer. Authors: Ljiljana Sjekloća / Regina Pudas / Björn Sjöblom / Peter Konarev / Oliviero Carugo / Vladimir Rybin / Tiila-Riikka Kiema / Dmitri Svergun / Jari Ylänne / Kristina Djinović Carugo / Abstract: Filamin C is a dimeric, actin-binding protein involved in organization of cortical cytoskeleton and of the sarcomere. We performed crystallographic, small-angle X-ray scattering and analytical ...Filamin C is a dimeric, actin-binding protein involved in organization of cortical cytoskeleton and of the sarcomere. We performed crystallographic, small-angle X-ray scattering and analytical ultracentrifugation experiments on the constructs containing carboxy-terminal domains of the protein (domains 23-24 and 19-21). The crystal structure of domain 23 of filamin C showed that the protein adopts the expected immunoglobulin (Ig)-like fold. Small-angle X-ray scattering experiments performed on filamin C tandem Ig-like domains 23 and 24 reveal a dimer that is formed by domain 24 and that domain 23 has little interactions with itself or with domain 24, while the analytical ultracentrifugation experiments showed that the filamin C domains 19-21 form elongated monomers in diluted solutions.
History
Deposition
Oct 31, 2006
Deposition site: RCSB / Processing site: PDBJ
Revision 1.0
Sep 11, 2007
Provider: repository / Type: Initial release
Revision 1.1
Jul 13, 2011
Group: Non-polymer description / Version format compliance
Resolution: 2.05→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.1 / Num. unique all: 950 / Rsym value: 0.298 / % possible all: 97.7
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
MAR345
datacollection
DENZO
datareduction
SCALA
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.05→45.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.855 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
329
4.7 %
RANDOM
Rwork
0.188
-
-
-
all
0.19
7116
-
-
obs
0.19
7016
97.51 %
-
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: 36.963 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.55 Å2
0.28 Å2
0 Å2
2-
-
0.55 Å2
0 Å2
3-
-
-
-0.83 Å2
Refinement step
Cycle: LAST / Resolution: 2.05→45.17 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
689
0
23
56
768
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
712
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
651
X-RAY DIFFRACTION
r_angle_refined_deg
1.288
2.018
966
X-RAY DIFFRACTION
r_angle_other_deg
0.728
3
1519
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.543
5
96
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.058
24.737
19
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.785
15
95
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
7.013
15
1
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
109
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
798
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
131
X-RAY DIFFRACTION
r_nbd_refined
0.181
0.2
85
X-RAY DIFFRACTION
r_nbd_other
0.229
0.2
539
X-RAY DIFFRACTION
r_nbtor_refined
0.173
0.2
323
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
403
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.113
0.2
34
X-RAY DIFFRACTION
r_metal_ion_refined
0.026
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.11
0.2
4
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.259
0.2
19
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.098
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
1.34
1.5
605
X-RAY DIFFRACTION
r_mcbond_other
0.191
1.5
203
X-RAY DIFFRACTION
r_mcangle_it
1.554
2
766
X-RAY DIFFRACTION
r_scbond_it
2.379
3
267
X-RAY DIFFRACTION
r_scangle_it
3.207
4.5
200
LS refinement shell
Resolution: 2.05→2.104 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.219
19
-
Rwork
0.213
485
-
obs
-
504
94.38 %
+
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