SAXSdb — 2btq

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

TUBULIN BTUBA

PROSTHECOBACTER DEJONGEII

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–473	Not recorded	TUBULIN BTUBB × 2 （Q8GCC1） 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

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 2BTQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BTO Structure of BtubA from Prosthecobacter dejongeii Deposited 2005-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–473（473 aa） Chain B 1–473（473 aa）	Not recorded	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
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

TUBULIN BTUBB

PROSTHECOBACTER DEJONGEII

UniProt Q8GCC1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–426	Not recorded	TUBULIN BTUBA × 2 （Q8GCC5） 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

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 2BTQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 1B 1–426（426 aa） Chain 2B 1–426（426 aa） Chain 3B 1–426（426 aa） Chain 4B 1–426（426 aa） Chain 5B 1–426（426 aa） Chain 6B 1–426（426 aa） Chain 7B 1–426（426 aa） Chain 8B 1–426（426 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8GCC1_9BACT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–426； UniProt 1–426

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2btq
Deposition date deposition_date	2005-06-06
Structure title title	Structure of BtubAB heterodimer from Prosthecobacter dejongeii
Keywords keywords	;STRUCTURAL PROTEIN, CYTOSKELETAL PROTEIN-COMPLEX, BACTERIAL TUBULIN, CYTOSKELETON, POLYMERIZATION, VERRUCOMICROBIA, PROTEIN COMPLEX, CYTOSKELETAL PROTEIN ;; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.11 Å
Radius of gyration Rg (electron density) rg_electron	29.33 Å
Forward intensity I(0) i0	132296000.00
Molecular weight molecular_weight	91040.0 kDa
Excluded volume excluded_volume	113820 Å³
Envelope volume envelope_volume	136810 Å³
Hydration-shell volume shell_volume	38716 Å³
Envelope diameter envelope_diameter	105.0 Å
Shell Rg shell_rg	36.76 Å
Envelope Rg envelope_rg	29.60 Å
Shape Rg shape_rg	29.35 Å
Total Rg total_rg	29.90 Å
Total atoms total_atoms	6402
Residues n_residues	828
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	100.9 Å
Rg (real space) rg_real	30.15 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	1.3230e+08
I(0) uncertainty (real space) i0_real_error	1.8490e+06
Rg (reciprocal space) rg_reciprocal	30.14 Å
I(0) (reciprocal space) i0_reciprocal	132300000.0000
Solution quality estimate total_estimate	0.8763
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33280000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	TUBULIN BTUBA
Molecular weight formula_weight	51299.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6402

MKVNNTIVVSIGQAGNQIAASFWKTVCLEHGIDPLTGQTAPGVAPRGNWSSFFSKLGESSSGSYVPRAIMVDLEPSVIDNVKATSGSLFNPANLISRTEGAGGNFAVGYLGAGREVLPEVMSRLDYEIDKCDNVGGIIVLHAIGGGTGSGFGALLIESLKEKYGEIPVLSCAVLPSPQVSSVVTEPYNTVFALNTLRRSADACLIFDNEALFDLAHRKWNIESPTVDDLNLLITEALAGITASMRFSGFLTVEISLRELLTNLVPQPSLHFLMCAFAPLTPPDRSKFEELGIEEMIKSLFDNGSVFAACSPMEGRFLSTAVLYRGIMEDKPLADAALAAMREKLPLTYWIPTAFKIGYVEQPGISHRKSMVLLANNTEIARVLDRICHNFDKLWQRKAFANWYLNEGMSEEQINVLRASAQELVQSYQVAEESGAKAKVQDSAGDTGMRAAAAGVSDDARGSMSLRDLVDRRR

来源 Source

来源生物 organism	PROSTHECOBACTER DEJONGEII
NCBI Class编号 ncbi_taxonomy_id	48465
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	TUBULIN BTUBB
Molecular weight formula_weight	46465.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VREILSIHVGQCGNQIADSFWRLALREHGLTEAGTLKEGSNAAANSNMEVFFHKVRDGKYVPRAVLVDLEPGVIARIEGGDMSQLFDESSIVRKIPGAANNWARGYNVEGEKVIDQIMNVIDSAVEKTKGLQGFLMTHSIGGGSGSGLGSLILERLRQAYPKKRIFTFSVVPSPLISDSAVEPYNAILTLQRILDNADGAVLLDNEALFRIAKAKLNRSPNYMDLNNIIALIVSSVTASLRFPGKLNTDLSEFVTNLVPFPGNHFLTASFAPMRGAGQEGQVRTNFPDLARETFAQDNFTAAIDWQQGVYLAASALFRGDVKAKDVDENMATIRKSLNYASYMPASGGLKLGYAETAPEGFASSGLALVNHTGIAAVFERLIAQFDIMFDNHAYTHWYENAGVSRDMMAKARNQIATLAQSYRDAS

来源 Source

来源生物 organism	PROSTHECOBACTER DEJONGEII
NCBI Class编号 ncbi_taxonomy_id	48465
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2btqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
Family Family family	c.32.1.1 — Tubulin, GTPase domain

Domain ID domain_id	d2btqa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
Family Family family	d.79.2.1 — Tubulin, C-terminal domain

CATH v4.4 (5 domains)

Domain ID domain_id	2btqA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	2btqA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	2btqB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	2btqB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	2btqB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

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8. Citations (1)

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Unit-cell length a length_a	154.398 Å
Unit-cell length b length_b	154.398 Å
Unit-cell length c length_c	256.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	53.520 Å
R factor r_factor	0.2147
R_work r_work	0.2147
R_free r_free	0.2466

fit	/app/data/saxs_computation/bt/2btq/2btq.fit
pddf	/app/data/pr_computation/bt/2btq/2btq.pr.out
profile	/app/data/saxs_computation/bt/2btq/2btq.dat

Structure of BtubAB heterodimer from Prosthecobacter dejongeii

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

TUBULIN BTUBA

State in the Current Structure

Other States of the Same Protein in the Database

TUBULIN BTUBB

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)