SAXSdb — 4f9k

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

cAMP-dependent protein kinase type I-beta regulatory subunit

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 11–73 Chain B； UniProt 11–73	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：microbatch under oil；pH 6.5；291 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.2M (NH4)2SO4, 0.1M Na-c, microbatch under oil, temperature 291K	Resolution 2.80 Å R-free 0.324
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 11–73 Chain D； UniProt 11–73	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：microbatch under oil；pH 6.5；291 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.2M (NH4)2SO4, 0.1M Na-c, microbatch under oil, temperature 291K	Resolution 2.80 Å R-free 0.324

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 4F9K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DIN Novel Localization and Quaternary Structure of the PKA RI beta Holoenzyme Deposited 2012-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–381（381 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；1.4 M ammonium sulfate, 0.1M Sodium Acetate pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.70 Å R-free 0.293
9O7V Crystal Structure of the RIb:C Heterodimer of PKA Deposited 2025-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–381（381 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1.4M ammonium sulfate and 0.1M sodium acetate at pH 5.3.	Resolution 3.70 Å R-free 0.293

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

View Construct and Data Evidence

UniProt name	KAP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 33–95； UniProt 11–73 Author chain B； PDBConstruct 33–95； UniProt 11–73 Author chain C； PDBConstruct 33–95； UniProt 11–73 Author chain D； PDBConstruct 33–95； UniProt 11–73

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	4f9k
Deposition date deposition_date	2012-05-18
Structure title title	Crystal Structure of human cAMP-dependent protein kinase type I-beta regulatory subunit (fragment 11-73), Northeast Structural Genomics Consortium (NESG) Target HR8613A
Keywords keywords	;Structural Genomics, PSI-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Transferase Regulator ;; Transferase Regulator
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	24.71 Å
Radius of gyration Rg (electron density) rg_electron	24.56 Å
Forward intensity I(0) i0	13777500.00
Molecular weight molecular_weight	27441.0 kDa
Excluded volume excluded_volume	34297 Å³
Envelope volume envelope_volume	45001 Å³
Hydration-shell volume shell_volume	17192 Å³
Envelope diameter envelope_diameter	100.4 Å
Shell Rg shell_rg	28.55 Å
Envelope Rg envelope_rg	25.22 Å
Shape Rg shape_rg	24.58 Å
Total Rg total_rg	25.10 Å
Total atoms total_atoms	1906
Residues n_residues	224
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	96.3 Å
Rg (real space) rg_real	25.17 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	1.3780e+07
I(0) uncertainty (real space) i0_real_error	2.4810e+05
Rg (reciprocal space) rg_reciprocal	25.06 Å
I(0) (reciprocal space) i0_reciprocal	13780000.0000
Solution quality estimate total_estimate	0.7214
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.686
Kurtosis Kurtosis kurtosis	-0.012
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1819000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.408; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.176; Smooth: 0.972

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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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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4f9ka_
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.0 — automated matches

Domain ID domain_id	d4f9kb_
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.0 — automated matches

Domain ID domain_id	d4f9kc_
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.0 — automated matches

Domain ID domain_id	d4f9kd_
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	4f9kA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4f9kB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4f9kC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4f9kD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

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8. Citations (1)

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Unit-cell length a length_a	82.270 Å
Unit-cell length b length_b	50.070 Å
Unit-cell length c length_c	75.600 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.300 Å
R factor r_factor	0.2570
R_work r_work	0.2540
R_free r_free	0.3240

Description description	cAMP-dependent protein kinase type I-beta regulatory subunit
Molecular weight formula_weight	11659.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1906

Crystal Structure of human cAMP-dependent protein kinase type I-beta regulatory subunit (fragment 11-73), Northeast Structural Genomics Consortium (NESG) Target HR8613A

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

cAMP-dependent protein kinase type I-beta regulatory subunit

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/f9/4f9k/4f9k.fit
pddf	/app/data/pr_computation/f9/4f9k/4f9k.pr.out
profile	/app/data/saxs_computation/f9/4f9k/4f9k.dat