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9u6d

Crystal structure of tubulin-RB3-TTL in complex with X8

Method: X-RAY DIFFRACTION D_max: 206.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u6d
deposition_date	2025-03-23
title	Crystal structure of tubulin-RB3-TTL in complex with X8
keywords	Tubulin, CELL CYCLE; CELL CYCLE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	55.43 Å
rg_electron	56.37 Å
i0	892938000.00
molecular_weight	245570.0 kDa
excluded_volume	305380 Å³
envelope_volume	405850 Å³
shell_volume	65810 Å³
envelope_diameter	198.3 Å
shell_rg	50.12 Å
envelope_rg	56.69 Å
shape_rg	56.35 Å
total_rg	56.26 Å
total_atoms	33889
n_residues	2163
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	206.5 Å
rg_real	56.17 Å
rg_real_error	3.31 Å
i0_real	8.9290e+08
i0_real_error	2.1950e+07
rg_reciprocal	54.78 Å
i0_reciprocal	891100000.0000
total_estimate	0.7022
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	36.9 Å
skewness	0.573
kurtosis	-0.532
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	103900000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.333; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.326; Smooth: 0.799

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Tubulin alpha-1B chain
formula_weight	50204.4 kDa
ec_number	3.6.5.-
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	34334

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

description	Tubulin beta chain
formula_weight	48299.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD

Entity 3 polymer

description	Stathmin-4
formula_weight	22125.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MTLAAYKEKMKELPLVSLFCSCFLSDPLNKSSYKYEADTVDLNWCVISDMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKEEASR

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 4 polymer

description	Tubulin--tyrosine ligase
formula_weight	44378.5 kDa
ec_number	6.3.2.25
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQLVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLINNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVHVIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHLTNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEPAISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFPLADTGQKTSQPTSIFIKLHHHHHH

Source

organism	Gallus gallus
common_name	chicken
ncbi_taxonomy_id	9031
host_organism	Escherichia coli

Entity 5 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

Entity 7 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	6

Entity 8 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	;2-[2-fluoranyl-4-[4-[2-[4-[(1~{R},2~{S})-2-fluoranylcyclopropyl]carbonylpiperazin-1-yl]ethoxy]phenyl]phenyl]-~{N}-(phenylmethyl)ethanamide ;
formula_weight	533.6 kDa
src_method	syn
entity_count	2

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	428

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6. Citations (1)

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length_a	104.850 Å
length_b	157.580 Å
length_c	181.400 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.540 Å
resolution_low	62.990 Å
r_factor	0.2105
r_work	0.2090
r_free	0.2376

fit	/app/data/saxs_computation/u6/9u6d/9u6d.fit
pddf	/app/data/pr_computation/u6/9u6d/9u6d.pr.out
profile	/app/data/saxs_computation/u6/9u6d/9u6d.dat

Crystal structure of tubulin-RB3-TTL in complex with X8

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)