SEQUENCE THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN ...SEQUENCE THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D) AND ONE STATHMIN-LIKE DOMAIN OF RB3. AS THE SEQUENCE OF BOVINE BRAIN TUBULIN IS NOT AVAILABLE, THE PIG BRAIN TUBULIN SEQUENCE WAS USED AS A REFERENCE. ONE NOTICEABLE EXCEPTION IS RESIDUE ALPHA 265 WHICH IS COMMONLY ILE BUT ALA IN PIG ALPHA TUBULIN. ALPHA-TUBULIN AND BETA-TUBULIN HAVE BEEN ALIGNED AS IN NOGALES ET AL., NATURE VOL 391, PAGES 199-203. IN THIS ALIGNMENT, RESIDUES 45-46 AND 361-368 OF ALPHA-TUBULIN ARE MISSING IN BETA-TUBULIN. THE STATHMIN-LIKE DOMAIN OF RB3 (RB3-SLD) CORRESPONDS TO STAHMIN RESIDUES 5 TO 145 WITH THE ADDITION OF ONE ALANINE AT THE N-TERMINUS, WHICH IS ACETYLATED. THE NUMBERING OF RB3-SLD IS ACCORDING TO THE STATHMIN SEQUENCE.
THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D) AND ONE STATHMIN-LIKE DOMAIN OF RB3
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Components
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Protein , 3 types, 5 molecules ACBDE
#1: Protein
Tubulinalphachain
Mass: 50163.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P02550, UniProt: Q2HJ86*PLUS
#2: Protein
Tubulinbetachain
Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P02554, UniProt: Q6B856*PLUS
#3: Protein
Stathmin4 / Stathmin-like protein B3 / RB3
Mass: 16712.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: STMN4 / Plasmid: pET-8c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63043
Resolution: 3.5→3.58 Å / Rmerge(I) obs: 0.639 / % possible all: 0.9
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 40 Å / Num. obs: 41617 / % possible obs: 96.4 %
Reflection shell
*PLUS
% possible obs: 82.4 % / Mean I/σ(I) obs: 1.5
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Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
SHELXD
phasing
SHARP
phasing
DM
modelbuilding
REFMAC
5.1.24
refinement
DM
phasing
Refinement
Method to determine structure: MIRAS / Resolution: 3.58→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / SU B: 33.422 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (3.58 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: ...Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (3.58 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: RESIDUES 38 TO 46 AND THE C-TERMINUS STARTING FROM RESIDUE 438 ON ALPHA TUBULIN CHAIN A, RESIDUES 278 TO 285 AND THE C-TERMINUS STARTING FROM RESIDUE 439 ON BETA TUBULIN CHAIN B, RESIDUES 37 TO 46, 280 TO 284, AND THE THE C-TERMINUS STARTING FROM RESIDUE 438 ON ALPHA TUBULIN CHAIN C, RESIDUES 278 TO 285 AND THE C-TERMINUS STARTING FROM RESIDUES 439 ON BETA TUBULIN CHAIN D, AND RESIDUES 31 TO 44 AND 142 TO 145 OF RB3-SLD. CA 5% OF THE SIDE CHAINS ARE POORLY DEFINED AND ARE CURRENTLY MODELLED AS ALANINES.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24852
2042
5.1 %
RANDOM
Rwork
0.23166
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-
-
all
0.23252
-
-
-
obs
0.23252
38029
98.79 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 83.054 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.89 Å2
0.44 Å2
0 Å2
2-
-
0.89 Å2
0 Å2
3-
-
-
-1.33 Å2
Refinement step
Cycle: LAST / Resolution: 3.58→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13891
0
183
0
14074
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.021
14384
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.975
1.954
19570
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.148
5
1798
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.138
0.2
2161
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
11067
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.286
0.2
6934
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
0.202
0.2
466
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.173
0.2
2
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.337
0.2
44
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_mcbond_it
0
1.5
8994
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0
2
14414
X-RAY DIFFRACTION
r_scbond_it
0
3
5390
X-RAY DIFFRACTION
r_scangle_it
0
4.5
5156
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
3060
tightpositional
0.05
0.05
2
B
3216
tightpositional
0.04
0.05
1
A
3060
tightthermal
0
0.5
2
B
3216
tightthermal
0
0.5
LS refinement shell
Resolution: 3.58→3.67 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.332
135
Rwork
0.365
2530
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
7.464
0.723
0.2838
3.1906
-0.106
2.8207
0.0868
-0.3324
0.7608
0.025
-0.1473
-0.2677
-0.2291
0.0761
0.0605
0.3413
-0.1397
0.0621
0.5176
0.0115
0.6192
136.126
104.796
16.916
2
8.197
1.9446
-0.4582
3.9983
-0.4761
3.872
-0.0926
0.1171
-0.6302
-0.3351
-0.07
-0.3749
0.5417
0.0428
0.1626
0.4252
-0.1643
-0.0207
1.0191
0.0794
0.3807
103.423
80.074
4.65
3
8.358
1.8735
-0.4362
4.0163
-0.3901
3.495
0.024
0.415
-0.4951
-0.3384
0.1323
-0.6699
0.1152
0.6136
-0.1563
0.4361
-0.1656
-0.2006
1.156
0.139
0.6129
64.872
60.262
-2.935
4
7.8645
1.1417
-0.5408
4.5023
-0.4684
5.4019
0.0183
0.4949
-0.1528
-0.2767
-0.2168
0.2836
0.4711
-0.0344
0.1985
0.343
-0.0365
-0.3953
1.0915
0.0909
0.5632
25.495
46.997
-5.531
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
2 - 437
2 - 437
2
X-RAY DIFFRACTION
1
E
E
4 - 30
1 - 27
3
X-RAY DIFFRACTION
2
B
B
2 - 438
2 - 428
4
X-RAY DIFFRACTION
2
E
E
65 - 89
62 - 86
5
X-RAY DIFFRACTION
3
C
C
2 - 437
2 - 437
6
X-RAY DIFFRACTION
3
E
E
90 - 115
87 - 112
7
X-RAY DIFFRACTION
4
D
D
2 - 438
2 - 428
8
X-RAY DIFFRACTION
4
E
E
116 - 141
113 - 138
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
+
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