SAXSdb — 5g4f

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

VCP-LIKE ATPASE

THERMOPLASMA ACIDOPHILUM

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–726 Chain B； UniProt 1–726 Chain C； UniProt 1–726 Chain D； UniProt 1–726 Chain E； UniProt 1–726 Chain P； UniProt 1–726	Not recorded	No other associated polymer	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

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 5G4F	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 oligomeric state 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 oligomeric state 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
5G4G Structure of the ATPgS-bound VAT complex Deposited 2016-05-12	Different construct 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 ligand/ion 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 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
7DBO DPBB domain of VCP-like ATPase from Thermoplasma acidophilum Deposited 2020-10-21	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 1–91（91 aa）	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
7DBO DPBB domain of VCP-like ATPase from Thermoplasma acidophilum Deposited 2020-10-21	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 1–91（91 aa）	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

6 other PDB entries and 7 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 1–726； UniProt 1–726 Author chain B； PDBConstruct 1–726； UniProt 1–726 Author chain C； PDBConstruct 1–726； UniProt 1–726 Author chain D； PDBConstruct 1–726； UniProt 1–726 Author chain E； PDBConstruct 1–726； UniProt 1–726 Author chain P； PDBConstruct 1–726； UniProt 1–726

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	5g4f
Deposition date deposition_date	2016-05-12
Structure title title	Structure of the ADP-bound VAT complex
Keywords keywords	HYDROLASE, VAT, PROTEASOME, PROTEIN DYNAMICS, UNFOLDASE, CONFORMATIONS, AAA ATPASE; HYDROLASE
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	54.35 Å
Radius of gyration Rg (electron density) rg_electron	53.84 Å
Forward intensity I(0) i0	3279230000.00
Molecular weight molecular_weight	485270.0 kDa
Excluded volume excluded_volume	610700 Å³
Envelope volume envelope_volume	877980 Å³
Hydration-shell volume shell_volume	130130 Å³
Envelope diameter envelope_diameter	170.9 Å
Shell Rg shell_rg	61.67 Å
Envelope Rg envelope_rg	52.41 Å
Shape Rg shape_rg	53.81 Å
Total Rg total_rg	54.14 Å
Total atoms total_atoms	69210
Residues n_residues	4356
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	168.6 Å
Rg (real space) rg_real	54.08 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	3.2790e+09
I(0) uncertainty (real space) i0_real_error	6.1330e+07
Rg (reciprocal space) rg_reciprocal	54.56 Å
I(0) (reciprocal space) i0_reciprocal	3281000000.0000
Solution quality estimate total_estimate	0.8751
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.7 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.522
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	292200000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.640

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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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	1

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

Resolution resolution	7.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	7.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	71258

Description description	VCP-LIKE ATPASE
Molecular weight formula_weight	81001.2 kDa
Source method src_method	man
Copy count entity_count	6

Structure of the ADP-bound VAT complex

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,P
Atom count atom_count	69210

来源生物 organism	THERMOPLASMA ACIDOPHILUM
NCBI Class编号 ncbi_taxonomy_id	2303
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/g4/5g4f/5g4f.fit
pddf	/app/data/pr_computation/g4/5g4f/5g4f.pr.out
profile	/app/data/saxs_computation/g4/5g4f/5g4f.dat