SAXSdb — 1cja

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

PROTEIN (ACTIN-FRAGMIN KINASE)

Physarum polycephalum

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 2–343	Fragment：CATALYTIC DOMAIN	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；2.0 M LI2SO4, 0.1 M MES, PH 6.0	Resolution 2.90 Å R-free 0.272
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–343	Fragment：CATALYTIC DOMAIN	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；2.0 M LI2SO4, 0.1 M MES, PH 6.0	Resolution 2.90 Å R-free 0.272

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q94706_PHYPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–342； UniProt 2–343 Author chain B； PDBConstruct 1–342； UniProt 2–343

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	1cja
Deposition date deposition_date	1999-04-08
Structure title title	ACTIN-FRAGMIN KINASE, CATALYTIC DOMAIN FROM PHYSARUM POLYCEPHALUM
Keywords keywords	KINASE, ACTIN, TRANSFERASE; TRANSFERASE
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	33.93 Å
Radius of gyration Rg (electron density) rg_electron	33.89 Å
Forward intensity I(0) i0	84839000.00
Molecular weight molecular_weight	73322.0 kDa
Excluded volume excluded_volume	91814 Å³
Envelope volume envelope_volume	115590 Å³
Hydration-shell volume shell_volume	30287 Å³
Envelope diameter envelope_diameter	116.1 Å
Shell Rg shell_rg	37.85 Å
Envelope Rg envelope_rg	33.83 Å
Shape Rg shape_rg	33.90 Å
Total Rg total_rg	34.15 Å
Total atoms total_atoms	6286
Residues n_residues	654
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	115.3 Å
Rg (real space) rg_real	34.23 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	8.4840e+07
I(0) uncertainty (real space) i0_real_error	1.6070e+06
Rg (reciprocal space) rg_reciprocal	34.05 Å
I(0) (reciprocal space) i0_reciprocal	84830000.0000
Solution quality estimate total_estimate	0.7846
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.493
Kurtosis Kurtosis kurtosis	-0.573
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42460000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.496; Smooth: 0.771

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cjaa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.3 — Actin-fragmin kinase, catalytic domain

Domain ID domain_id	d1cjab_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.3 — Actin-fragmin kinase, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1cjaA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	1cjaA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

Domain ID domain_id	1cjaB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	1cjaB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	178.900 Å
Unit-cell length b length_b	178.900 Å
Unit-cell length c length_c	59.300 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	0.2720

Description description	PROTEIN (ACTIN-FRAGMIN KINASE)
Molecular weight formula_weight	38099.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6286

ACTIN-FRAGMIN KINASE, CATALYTIC DOMAIN FROM PHYSARUM POLYCEPHALUM

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

PROTEIN (ACTIN-FRAGMIN KINASE)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Physarum polycephalum
NCBI Class编号 ncbi_taxonomy_id	5791
宿主生物 host_organism	Escherichia coli

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

fit	/app/data/saxs_computation/cj/1cja/1cja.fit
pddf	/app/data/pr_computation/cj/1cja/1cja.pr.out
profile	/app/data/saxs_computation/cj/1cja/1cja.dat