SAXSdb — 5o09

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

Tubulin

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain 1A； UniProt 3–435 Chain 2A； UniProt 3–435 Chain 3A； UniProt 3–435 Chain 4A； UniProt 3–435 Chain 5A； UniProt 3–435 Chain 6A； UniProt 3–435 Chain 7A； UniProt 3–435 Chain 8A； UniProt 3–435	Not recorded	Tubulin BtubB × 8 （Q8GCC1） Bacterial kinesin light chain × 8 （A8Y5U5） GDP GUANOSINE-5'-DIPHOSPHATE × 16	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

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 5O09	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 method 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
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 method 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

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 1A； PDBConstruct 1–433； UniProt 3–435 Author chain 2A； PDBConstruct 1–433； UniProt 3–435 Author chain 3A； PDBConstruct 1–433； UniProt 3–435 Author chain 4A； PDBConstruct 1–433； UniProt 3–435 Author chain 5A； PDBConstruct 1–433； UniProt 3–435 Author chain 6A； PDBConstruct 1–433； UniProt 3–435 Author chain 7A； PDBConstruct 1–433； UniProt 3–435 Author chain 8A； PDBConstruct 1–433； UniProt 3–435

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain 1B； UniProt 1–426 Chain 2B； UniProt 1–426 Chain 3B； UniProt 1–426 Chain 4B； UniProt 1–426 Chain 5B； UniProt 1–426 Chain 6B； UniProt 1–426 Chain 7B； UniProt 1–426 Chain 8B； UniProt 1–426	Not recorded	Tubulin × 8 （Q8GCC5） Bacterial kinesin light chain × 8 （A8Y5U5） GDP GUANOSINE-5'-DIPHOSPHATE × 16	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

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 5O09	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–426（426 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

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 1B； PDBConstruct 1–426； UniProt 1–426 Author chain 2B； PDBConstruct 1–426； UniProt 1–426 Author chain 3B； PDBConstruct 1–426； UniProt 1–426 Author chain 4B； PDBConstruct 1–426； UniProt 1–426 Author chain 5B； PDBConstruct 1–426； UniProt 1–426 Author chain 6B； PDBConstruct 1–426； UniProt 1–426 Author chain 7B； PDBConstruct 1–426； UniProt 1–426 Author chain 8B； PDBConstruct 1–426； UniProt 1–426

Bacterial kinesin light chain

Prosthecobacter vanneervenii

UniProt A8Y5U5

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain 1C； UniProt 2–239 Chain 2C； UniProt 2–239 Chain 3C； UniProt 2–239 Chain 4C； UniProt 2–239 Chain 5C； UniProt 2–239 Chain 6C； UniProt 2–239 Chain 7C； UniProt 2–239 Chain 8C； UniProt 2–239	Not recorded	Tubulin × 8 （Q8GCC5） Tubulin BtubB × 8 （Q8GCC1） GDP GUANOSINE-5'-DIPHOSPHATE × 16	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

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 5O09	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5O01 Crystal structure of BtubC (BKLC) from P. vanneervenii Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–256（256 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；50 mM CHES/NaOH, 500 mM NaCl, 1 mM TCEP, 5% glycerol, pH 9.0	Resolution 2.50 Å R-free 0.237
5O01 Crystal structure of BtubC (BKLC) from P. vanneervenii Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–256（256 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；50 mM CHES/NaOH, 500 mM NaCl, 1 mM TCEP, 5% glycerol, pH 9.0	Resolution 2.50 Å R-free 0.237

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

View Construct and Data Evidence

UniProt name	A8Y5U5_9BACT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 1C； PDBConstruct 1–238； UniProt 2–239 Author chain 2C； PDBConstruct 1–238； UniProt 2–239 Author chain 3C； PDBConstruct 1–238； UniProt 2–239 Author chain 4C； PDBConstruct 1–238； UniProt 2–239 Author chain 5C； PDBConstruct 1–238； UniProt 2–239 Author chain 6C； PDBConstruct 1–238； UniProt 2–239 Author chain 7C； PDBConstruct 1–238； UniProt 2–239 Author chain 8C； PDBConstruct 1–238； UniProt 2–239

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	5o09
Deposition date deposition_date	2017-05-16
Structure title title	BtubABC mini microtubule
Keywords keywords	bacterial cytoskeleton, microtubules, structural protein; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	69.65 Å
Radius of gyration Rg (electron density) rg_electron	69.09 Å
Forward intensity I(0) i0	12885700000.00
Molecular weight molecular_weight	958310.0 kDa
Excluded volume excluded_volume	1197000 Å³
Envelope volume envelope_volume	1782100 Å³
Hydration-shell volume shell_volume	205870 Å³
Envelope diameter envelope_diameter	236.5 Å
Shell Rg shell_rg	77.20 Å
Envelope Rg envelope_rg	66.92 Å
Shape Rg shape_rg	69.10 Å
Total Rg total_rg	69.16 Å
Total atoms total_atoms	67424
Residues n_residues	8648
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	231.3 Å
Rg (real space) rg_real	69.40 Å
Rg uncertainty (real space) rg_real_error	2.83 Å
I(0) (real space) i0_real	1.2890e+10
I(0) uncertainty (real space) i0_real_error	3.0210e+08
Rg (reciprocal space) rg_reciprocal	70.45 Å
I(0) (reciprocal space) i0_reciprocal	12910000000.0000
Solution quality estimate total_estimate	0.8460
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	84.1 Å
Skewness Skewness skewness	0.151
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	674400000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.750

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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
Molecular weight formula_weight	47071.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1A,2A,3A,4A,5A,6A,7A,8A
Atom count atom_count	67424

VNNTIVVSIGQAGNQIAASFWKTVCLEHGIDPLTGQTAPGVAPRGNWSSFFSKLGESSSGSYVPRAIMVDLEPSVIDNVKATSGSLFNPANLISRTEGAGGNFAVGYLGAGREVLPEVMSRLDYEIDKCDNVGGIIVLHAIGGGTGSGFGALLIESLKEKYGEIPVLSCAVLPSPQVSSVVTEPYNTVFALNTLRRSADACLIFDNEALFDLAHRKWNIESPTVDDLNLLITEALAGITASMRFSGFLTVEITLRELLTNLVPQPSLHFLMCAFAPLTPPDRSKFEELGIEEMIKSLFDNGSVFAACSPMEGRFLSTAVLYRGIMEDKPLADAALAAMREKLPLTYWIPTAFKIGYVEQPGISHRKSMVLLANNTEIARVLDRICHNFDKLWQRKAFANWYLNEGMSEEQINVLRASAQELVQSYQVAEESGA

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

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	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1B,2B,3B,4B,5B,6B,7B,8B

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

Entity 3 Entity 3 polymer

Description description	Bacterial kinesin light chain
Molecular weight formula_weight	27135.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1C,2C,3C,4C,5C,6C,7C,8C

DTALERQIASASRSVEEARRLAYHDPIRVGALVEQISVLADLRQKEGDFRKAESLYREALFRAQELRKQDPDLLTGIYSLLAHLYDRWGRMDKAAEFYELALKISAENGLEESDKVATIKNNLAMIFKQLRKFERAEGYYCEALETFQRLDGEQSARVASVYNNLGVLYYSHMDVDRAQVMHERALAIRQNLHEGQMDPADLSQTFINLGAVYKAAGDFQKAEACVDRAKRIRAAMNG

来源 Source

来源生物 organism	Prosthecobacter vanneervenii
NCBI Class编号 ncbi_taxonomy_id	48466
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	16

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	257661

fit	/app/data/saxs_computation/o0/5o09/5o09.fit
pddf	/app/data/pr_computation/o0/5o09/5o09.pr.out
profile	/app/data/saxs_computation/o0/5o09/5o09.dat

BtubABC mini microtubule

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

Tubulin

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

Bacterial kinesin light chain

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

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)