SAXSdb — 1bdy

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

PROTEIN KINASE C

Rattus norvegicus

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 1–123 Chain B； UniProt 1–123	Fragment：C2-DOMAIN Mutation：GLY-SER-HIS AT THE N-TERMINUS	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；PROTEIN WAS CRYSTALLISED FROM 20% PEG 4000, 0.2M NH4 ACETATE, 0.1M CITRATE, PH 5.6	Resolution 2.20 Å R-free 0.247

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	KPCD_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 1–123 Author chain B； PDBConstruct 1–123； UniProt 1–123

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	1bdy
Deposition date deposition_date	1998-05-11
Structure title title	C2 DOMAIN FROM PROTEIN KINASE C DELTA
Keywords keywords	PROTEIN KINASE C, C2 DOMAIN, CALCIUM, CALCIUM-BINDING, DUPLICATION, ATP-BINDING, TRANSFERASE; CALCIUM-BINDING
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	20.61 Å
Radius of gyration Rg (electron density) rg_electron	19.53 Å
Forward intensity I(0) i0	13008300.00
Molecular weight molecular_weight	27465.0 kDa
Excluded volume excluded_volume	34658 Å³
Envelope volume envelope_volume	43241 Å³
Hydration-shell volume shell_volume	18822 Å³
Envelope diameter envelope_diameter	74.5 Å
Shell Rg shell_rg	25.49 Å
Envelope Rg envelope_rg	20.02 Å
Shape Rg shape_rg	19.54 Å
Total Rg total_rg	20.42 Å
Total atoms total_atoms	2354
Residues n_residues	246
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	73.2 Å
Rg (real space) rg_real	20.59 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.3010e+07
I(0) uncertainty (real space) i0_real_error	1.6430e+05
Rg (reciprocal space) rg_reciprocal	20.60 Å
I(0) (reciprocal space) i0_reciprocal	13010000.0000
Solution quality estimate total_estimate	0.8513
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.011
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2641000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.985

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bdya_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.1 — PLC-like (P variant)

Domain ID domain_id	d1bdyb_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.1 — PLC-like (P variant)

CATH v4.4 (2 domains)

Domain ID domain_id	1bdyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	1bdyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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8. Citations (1)

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Unit-cell length a length_a	40.720 Å
Unit-cell length b length_b	60.690 Å
Unit-cell length c length_c	120.900 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1976
R_work r_work	0.1976
R_free r_free	0.2470

Description description	PROTEIN KINASE C
Molecular weight formula_weight	14014.2 kDa
EC 编号 ec_number	2.7.1.37
Mutation mutation	GLY-SER-HIS AT THE N-TERMINUS
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	2600

C2 DOMAIN FROM PROTEIN KINASE C DELTA

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

PROTEIN KINASE C

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 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

fit	/app/data/saxs_computation/bd/1bdy/1bdy.fit
pddf	/app/data/pr_computation/bd/1bdy/1bdy.pr.out
profile	/app/data/saxs_computation/bd/1bdy/1bdy.dat