SAXSdb — 7dbo

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

VCP-like ATPase

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–91	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；100mM citrate / phosphate pH5.0, 1.4M Ammonium sulfate	Resolution 1.90 Å R-free 0.264
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–91	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；100mM citrate / phosphate pH5.0, 1.4M Ammonium sulfate	Resolution 1.90 Å R-free 0.264

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 7DBO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CZ4 NMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE ATPASE OF THERMOPLASMA) Deposited 1999-09-01	Different construct Different mutation/modification 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 1–183（183 aa） Fragment：N-TERMINAL DOMAIN: M1 TO E183 FOLLOWED BY A DIGLYCINE SPACER	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT NMR sample composition 1.4 MM VAT-NU-15N,13C; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O NMR sample composition 1.2 MM VAT-N U-15N; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O	Resolution not provided
1CZ5 NMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE ATPASE OF THERMOPLASMA) Deposited 1999-09-01	Different construct Different mutation/modification 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 1–183（183 aa） Fragment：N-TERMINAL DOMAIN: M1 TO E183 FOLLOWED BY A DIGLYCINE SPACER	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT NMR sample composition 1.4 MM VAT-N U-15N,13C; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O NMR sample composition 1.2 MM VAT-N U-15N; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O	Resolution not provided
5G4F Structure of the ADP-bound VAT complex Deposited 2016-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–726（726 aa） Chain B 1–726（726 aa） Chain C 1–726（726 aa） Chain D 1–726（726 aa） Chain E 1–726（726 aa） Chain P 1–726（726 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 MM HEPES, 100 MM NACL, 5MM ADP；pH 7.5；50 MM HEPES, 100 MM NACL, 5MM ADP cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 4 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE HELD AT 4 DEGREES CELSIUS BEFORE FREEZING	Resolution 7.00 Å
5G4G Structure of the ATPgS-bound VAT complex Deposited 2016-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 6–726（721 aa） Chain B 6–726（721 aa） Chain C 6–726（721 aa） Chain D 6–726（721 aa） Chain E 6–726（721 aa） Chain F 6–726（721 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 MM HEPES, 100 MM NACL, 5MM ATPGS；pH 7.5；50 MM HEPES, 100 MM NACL, 5MM ATPGS cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 4 SECONDS BEFORE PLUNGING,	Resolution 7.80 Å
5VC7 VCP like ATPase from T. acidophilum (VAT) - conformation 1 Deposited 2017-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 183–745（563 aa） Fragment：UNP residues 183-745 Chain C 183–745（563 aa） Fragment：UNP residues 183-745 Chain D 183–745（563 aa） Fragment：UNP residues 183-745 Chain E 183–745（563 aa） Fragment：UNP residues 183-745 Chain F 183–745（563 aa） Fragment：UNP residues 183-745 Chain G 183–745（563 aa） Fragment：UNP residues 183-745	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot for 4 seconds before plunging	Resolution 3.90 Å
5VCA VCP like ATPase from T. acidophilum (VAT)-Substrate bound conformation Deposited 2017-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain M 183–745（563 aa） Fragment：UNP residues 183-745 Chain N 183–745（563 aa） Fragment：UNP residues 183-745 Chain O 183–745（563 aa） Fragment：UNP residues 183-745 Chain P 183–745（563 aa） Fragment：UNP residues 183-745 Chain Q 183–745（563 aa） Fragment：UNP residues 183-745 Chain R 183–745（563 aa） Fragment：UNP residues 183-745	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot for 4 seconds before plunging	Resolution 4.80 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAT_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–93； UniProt 1–91 Author chain B； PDBConstruct 3–93； UniProt 1–91

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	7dbo
Deposition date deposition_date	2020-10-21
Structure title title	DPBB domain of VCP-like ATPase from Thermoplasma acidophilum
Keywords keywords	Double psi beta barrel, CHAPERONE; CHAPERONE
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	18.27 Å
Radius of gyration Rg (electron density) rg_electron	17.37 Å
Forward intensity I(0) i0	10373100.00
Molecular weight molecular_weight	20928.0 kDa
Excluded volume excluded_volume	24990 Å³
Envelope volume envelope_volume	29373 Å³
Hydration-shell volume shell_volume	14771 Å³
Envelope diameter envelope_diameter	60.7 Å
Shell Rg shell_rg	22.56 Å
Envelope Rg envelope_rg	17.53 Å
Shape Rg shape_rg	17.30 Å
Total Rg total_rg	18.29 Å
Total atoms total_atoms	1428
Residues n_residues	172
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	63.8 Å
Rg (real space) rg_real	18.29 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.0370e+07
I(0) uncertainty (real space) i0_real_error	1.3430e+05
Rg (reciprocal space) rg_reciprocal	18.29 Å
I(0) (reciprocal space) i0_reciprocal	10370000.0000
Solution quality estimate total_estimate	0.8585
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.318
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2043000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	VCP-like ATPase
Molecular weight formula_weight	10509.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1524

GPMESNNGIILRVAEANSTDPGMSRVRLDESSRRLLDAEIGDVVEIEKVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVKVRKVR

来源 Source

来源生物 organism	Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
NCBI Class编号 ncbi_taxonomy_id	273075
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7dboA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	7dboB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

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8. Citations (2)

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Unit-cell length a length_a	118.800 Å
Unit-cell length b length_b	118.800 Å
Unit-cell length c length_c	68.200 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	41.070 Å
R factor r_factor	0.2217
R_work r_work	0.2168
R_free r_free	0.2642

fit	/app/data/saxs_computation/db/7dbo/7dbo.fit
pddf	/app/data/pr_computation/db/7dbo/7dbo.pr.out
profile	/app/data/saxs_computation/db/7dbo/7dbo.dat

DPBB domain of VCP-like ATPase from Thermoplasma acidophilum

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

VCP-like ATPase

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