SAXSdb — 7sog

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

Actophorin

Acanthamoeba castellanii

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 2–135	Mutation：S2P, H21K, Q22K, T27I, M30L, A32D, S33D, H41K, K53L, S54A, R59N, Q71E, T81V, T99A, T101S, S104A, V110D, A122D, S130K	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；PEG 8000, NISO4, MES pH6.5	Resolution 1.74 Å R-free 0.225
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–135	Mutation：S2P, H21K, Q22K, T27I, M30L, A32D, S33D, H41K, K53L, S54A, R59N, Q71E, T81V, T99A, T101S, S104A, V110D, A122D, S130K	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；PEG 8000, NISO4, MES pH6.5	Resolution 1.74 Å R-free 0.225

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 7SOG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AHQ RECOMBINANT ACTOPHORIN Deposited 1997-04-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–137（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20-25% PEG 8000, 100MM HEPES (PH7.5), 10% ISOPROPANOL, 1MM DTT	Resolution 2.30 Å R-free 0.320
1CNU PHOSPHORYLATED ACTOPHORIN FROM ACANTAMOEBA POLYPHAGA Deposited 1999-05-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–137（136 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.25 Å R-free 0.304
7RTX Actophorin grown in microgravity Deposited 2021-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–138（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；10 mg/mL protein, 0.1 M MOPS, 16% Polyethylene glycol (8,000)	Resolution 1.65 Å R-free 0.223

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

View Construct and Data Evidence

UniProt name	ACTP_ACACA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–135； UniProt 2–135 Author chain B； PDBConstruct 2–135； UniProt 2–135

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	7sog
Deposition date deposition_date	2021-10-30
Structure title title	Thermostable actophorin
Keywords keywords	MOTOR PROTEIN, MUTAGENESIS; MOTOR 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	22.57 Å
Radius of gyration Rg (electron density) rg_electron	21.79 Å
Forward intensity I(0) i0	15529800.00
Molecular weight molecular_weight	29662.0 kDa
Excluded volume excluded_volume	37088 Å³
Envelope volume envelope_volume	44973 Å³
Hydration-shell volume shell_volume	18121 Å³
Envelope diameter envelope_diameter	75.1 Å
Shell Rg shell_rg	27.14 Å
Envelope Rg envelope_rg	21.97 Å
Shape Rg shape_rg	21.77 Å
Total Rg total_rg	22.61 Å
Total atoms total_atoms	4101
Residues n_residues	262
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	73.9 Å
Rg (real space) rg_real	22.66 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.5530e+07
I(0) uncertainty (real space) i0_real_error	2.0180e+05
Rg (reciprocal space) rg_reciprocal	22.64 Å
I(0) (reciprocal space) i0_reciprocal	15530000.0000
Solution quality estimate total_estimate	0.8807
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.434
Kurtosis Kurtosis kurtosis	-0.452
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3803000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.991

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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	Actophorin
Molecular weight formula_weight	15183.1 kDa
Mutation mutation	S2P, H21K, Q22K, T27I, M30L, A32D, S33D, H41K, K53L, S54A, R59N, Q71E, T81V, T99A, T101S, S104A, V110D, A122D, S130K
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	4458

GPGIAVSDDCVQKFNELKLGKKHRYVIFKLNDDNTEVVVEKVGGPNATYEDFLAQLPENDCRYAIFDYEFEVDGGQRNKIVFILWAPDSAPIKSKMMYASSKDAIKKKLDGIQVEVQATDADEISEDAVKERAKK

来源 Source

来源生物 organism	Acanthamoeba castellanii
通用名 common_name	Amoeba
NCBI Class编号 ncbi_taxonomy_id	5755
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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8. Citations (1)

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Unit-cell length a length_a	53.720 Å
Unit-cell length b length_b	41.290 Å
Unit-cell length c length_c	55.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.740 Å
Low-resolution limit resolution_low	36.580 Å
R factor r_factor	0.1936
R_work r_work	0.1907
R_free r_free	0.2251

fit	/app/data/saxs_computation/so/7sog/7sog.fit
pddf	/app/data/pr_computation/so/7sog/7sog.pr.out
profile	/app/data/saxs_computation/so/7sog/7sog.dat

Thermostable actophorin

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

Actophorin

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