6i5c

Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex

Method: X-RAY DIFFRACTION Dmax: 184.6 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tubulin alpha-1B chain

Bos taurus

UniProt P81947

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–440 Chain C; UniProt 1–440 Not recorded Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) TUBULIN-TYROSINE LIGASE × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 5 CL CHLORIDE ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole Resolution 2.95 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

249 other PDB entries and 251 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–440; UniProt 1–440 Author chain C; PDBConstruct 1–440; UniProt 1–440

Tubulin beta-2B chain

Bos taurus

UniProt Q6B856

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–431 Chain D; UniProt 1–431 Not recorded Tubulin alpha-1B chain × 2 (P81947) Stathmin-4 × 1 (P63043) TUBULIN-TYROSINE LIGASE × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 5 CL CHLORIDE ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole Resolution 2.95 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

273 other PDB entries and 275 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB2B_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–431; UniProt 1–431 Author chain D; PDBConstruct 1–431; UniProt 1–431

Stathmin-4

Rattus norvegicus

UniProt P63043

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 77–212 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) TUBULIN-TYROSINE LIGASE × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 5 CL CHLORIDE ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole Resolution 2.95 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

287 other PDB entries and 287 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STMN4_RAT
Isoform P63043-3
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–136; UniProt 77–212

TUBULIN-TYROSINE LIGASE

Gallus gallus

UniProt E1BQ43

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 1–378 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 5 CL CHLORIDE ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole Resolution 2.95 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

241 other PDB entries and 241 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E1BQ43_CHICK
Isoform
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 1–378; UniProt 1–378

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6i5c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6i5c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6i5c
Deposition date deposition_date2018-11-13
Structure title titleLong wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex
Keywords keywordsTubulin complex, T2R-TTL, Long-wavelength native-SAD phasing, native-SAD, S-SAD, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier55.87
Radius of gyration Rg (electron density) rg_electron56.81
Forward intensity I(0) i0929292000.00
Molecular weight molecular_weight248610.0 kDa
Excluded volume excluded_volume308540 ų
Envelope volume envelope_volume410550 ų
Hydration-shell volume shell_volume66192 ų
Envelope diameter envelope_diameter196.8
Shell Rg shell_rg50.39
Envelope Rg envelope_rg56.80
Shape Rg shape_rg56.83
Total Rg total_rg56.58
Total atoms total_atoms17432
Residues n_residues2178
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax184.6
Rg (real space) rg_real56.61
Rg uncertainty (real space) rg_real_error2.37
I(0) (real space) i0_real9.2930e+08
I(0) uncertainty (real space) i0_real_error1.9390e+07
Rg (reciprocal space) rg_reciprocal55.22
I(0) (reciprocal space) i0_reciprocal927400000.0000
Solution quality estimate total_estimate0.7213
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.5
Skewness Skewness skewness0.557
Kurtosis Kurtosis kurtosis-0.554
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85570000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.594; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.576; Smooth: 0.015

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

7. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd6i5ca1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6i5ca2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6i5cb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6i5cb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6i5cc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6i5cc2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6i5cd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6i5cd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6i5ce_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.10 — Stathmin
Family Family familya.137.10.1 — Stathmin
Domain ID domain_idd6i5cf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.30 — PreATP-grasp domain
Superfamily Superfamily superfamilyc.30.1 — PreATP-grasp domain
Family Family familyc.30.1.9 — Tubulin tyrosine ligase (TTL) N-terminal domain-like
Domain ID domain_idd6i5cf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.10 — Tubulin tyrosine ligase (TTL) C-terminal domain-like
Domain ID domain_idd6i5cf3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (15 domains)

Domain ID domain_id6i5cA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6i5cA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6i5cA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6i5cB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6i5cB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6i5cB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6i5cC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6i5cC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6i5cC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6i5cD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6i5cD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6i5cD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6i5cE01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily30
Domain ID domain_id6i5cF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11480
Domain ID domain_id6i5cF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain

8. Citations (2)

9. Files and Curves (10)