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2bto

Structure of BtubA from Prosthecobacter dejongeii

Method: X-RAY DIFFRACTION Dmax: 99.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TUBULIN BTUBA

PROSTHECOBACTER DEJONGEII

UniProt Q8GCC5

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain A； UniProt 1–473 Chain B； UniProt 1–473 Not recorded THIOREDOXIN 1 × 3 （P00274） GTP GUANOSINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：1.6M NA K PHOSPHATE, PH 6.0 Resolution 2.50 Å R-free 0.235

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.

Other PDB Difference from Current Entry 2BTO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BTQ Structure of BtubAB heterodimer from Prosthecobacter dejongeii Deposited 2005-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–473（473 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.5M LI2SO4, 0.4M TRIS/HCL, PH 7.5
Resolution 3.20 Å R-free 0.247
5O09 BtubABC mini microtubule Deposited 2017-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain 1A 3–435（433 aa）
Chain 2A 3–435（433 aa）
Chain 3A 3–435（433 aa）
Chain 4A 3–435（433 aa）
Chain 5A 3–435（433 aa）
Chain 6A 3–435（433 aa）
Chain 7A 3–435（433 aa）
Chain 8A 3–435（433 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8GCC5_9BACT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–473； UniProt 1–473 Author chain B； PDBConstruct 1–473； UniProt 1–473

THIOREDOXIN 1

ESCHERICHIA COLI

UniProt P00274

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain T； UniProt 1–108 Not recorded TUBULIN BTUBA × 6 （Q8GCC5） GTP GUANOSINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：1.6M NA K PHOSPHATE, PH 6.0 Resolution 2.50 Å R-free 0.235

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.

Other PDB Difference from Current Entry 2BTO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M7T Solution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability Deposited 2002-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 68–107（40 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；308 K
NMR sample composition 1 mM protein in 100 mM sodium phosphate buffer (pH 7.0), 20 M EDTA, 0.02% sodium azide, and 10% D2O. | 90% H2O/10% D2O
Resolution not provided
1OAZ IgE Fv SPE7 complexed with a recombinant thioredoxin Deposited 2003-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–34（34 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Chain A 35–108（74 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00
Resolution 2.78 Å R-free 0.276
1OAZ IgE Fv SPE7 complexed with a recombinant thioredoxin Deposited 2003-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–34（34 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Chain B 35–108（74 aa） Fragment：TRX-SHEAR3, RESIDUES 1-123
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00
Resolution 2.78 Å R-free 0.276
1ZZY Crystal Structure of Thioredoxin Mutant L7V Deposited 2005-06-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–108（108 aa）
Mutation：L7V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；pH 3.8；295 K；10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K
Resolution 2.50 Å R-free 0.274
1ZZY Crystal Structure of Thioredoxin Mutant L7V Deposited 2005-06-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–108（108 aa）
Mutation：L7V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；pH 3.8；295 K；10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K
Resolution 2.50 Å R-free 0.274

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIO_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain T； PDBConstruct 1–108； UniProt 1–108

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 2bto

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bto
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bto
Deposition date deposition_date2005-06-04
Structure title titleStructure of BtubA from Prosthecobacter dejongeii
Keywords keywordsBACTERIAL TUBULIN, POLYMERIZATION, CYTOSKELETON, PROTEIN COMPLEX, CYTOSKELETAL PROTEIN; CYTOSKELETAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.14 Å
Radius of gyration Rg (electron density) rg_electron30.31 Å
Forward intensity I(0) i0165262000.00
Molecular weight molecular_weight102950.0 kDa
Excluded volume excluded_volume129150 ų
Envelope volume envelope_volume158980 ų
Hydration-shell volume shell_volume43171 ų
Envelope diameter envelope_diameter110.3 Å
Shell Rg shell_rg38.06 Å
Envelope Rg envelope_rg30.15 Å
Shape Rg shape_rg30.33 Å
Total Rg total_rg30.92 Å
Total atoms total_atoms7235
Residues n_residues939
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax99.0 Å
Rg (real space) rg_real31.07 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real1.6530e+08
I(0) uncertainty (real space) i0_real_error2.6490e+06
Rg (reciprocal space) rg_reciprocal31.11 Å
I(0) (reciprocal space) i0_reciprocal165300000.0000
Solution quality estimate total_estimate0.8980
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9 Å
Skewness Skewness skewness0.287
Kurtosis Kurtosis kurtosis-0.428
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39950000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.915
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2btoa1
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_idd2btoa2
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_idd2btob1
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_idd2btob2
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_idd2btot_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.1 — Thioltransferase

CATH v4.4 (7 domains)

Domain ID domain_id2btoA01
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_id2btoA02
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_id2btoA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id2btoB01
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_id2btoB02
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_id2btoB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id2btoT00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
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8. Citations (1)

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9. Files and Curves (10)