SAXSdb — 1n0y

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

Calmodulin

Paramecium tetraurelia

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 1–148	Not recorded	PB LEAD (II) ION × 7 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；MPD, sodium cacodylate, sodium acetate, lead nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.223
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–148	Not recorded	PB LEAD (II) ION × 7 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；MPD, sodium cacodylate, sodium acetate, lead nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.223

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 1N0Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CLM STRUCTURE OF PARAMECIUM TETRAURELIA CALMODULIN AT 1.8 ANGSTROMS RESOLUTION Deposited 1993-01-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1EXR THE 1.0 ANGSTROM CRYSTAL STRUCTURE OF CA+2 BOUND CALMODULIN Deposited 2000-05-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；278 K；MPD, calcium chloride, sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 1.00 Å R-free 0.163
1OSA CRYSTAL STRUCTURE OF RECOMBINANT PARAMECIUM TETRAURELIA CALMODULIN AT 1.68 ANGSTROMS RESOLUTION Deposited 1993-08-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.68 Å
2KXW Structure of the C-domain Fragment of apo Calmodulin Bound to the IQ motif of Nav1.2 Deposited 2010-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–149（73 aa） Fragment：C-domain (UNP Residues 77-149)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 1.5 mM Voltage-dependent Sodium Channel v 1.2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM Voltage-dependent Sodium Channel v 1.2, 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 100% D2O \| 100% D2O	Resolution not provided
2M5E Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2 Deposited 2013-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–149（73 aa） Fragment：UNP residues 77-149	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 100% D2O \| 100% D2O	Resolution not provided
5E1K Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia SAD data Deposited 2015-09-29	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 2–149（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；50 mM sodium cacodylate, 50% MPD	Resolution 1.00 Å R-free 0.165
5E1N Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia qFit disorder model Deposited 2015-09-29	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 2–149（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；50 mM sodium cacodylate, 50% MPD	Resolution 1.00 Å R-free 0.150
5E1P Ca(2+)-Calmodulin from Paramecium tetraurelia qFit disorder model Deposited 2015-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；50 mM sodium cacodylate, 50% MPD	Resolution 1.01 Å R-free 0.142

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM_PARTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–148； UniProt 1–148 Author chain B； PDBConstruct 1–148； UniProt 1–148

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	1n0y
Deposition date deposition_date	2002-10-15
Structure title title	Crystal Structure of Pb-bound Calmodulin
Keywords keywords	calmodulin, lead, metal binding protein; METAL BINDING 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	20.66 Å
Radius of gyration Rg (electron density) rg_electron	19.14 Å
Forward intensity I(0) i0	14026800.00
Molecular weight molecular_weight	21858.0 kDa
Excluded volume excluded_volume	23685 Å³
Envelope volume envelope_volume	31128 Å³
Hydration-shell volume shell_volume	14872 Å³
Envelope diameter envelope_diameter	68.6 Å
Shell Rg shell_rg	23.66 Å
Envelope Rg envelope_rg	18.90 Å
Shape Rg shape_rg	18.47 Å
Total Rg total_rg	21.00 Å
Total atoms total_atoms	1334
Residues n_residues	166
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	66.7 Å
Rg (real space) rg_real	20.67 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.4030e+07
I(0) uncertainty (real space) i0_real_error	1.8480e+05
Rg (reciprocal space) rg_reciprocal	20.67 Å
I(0) (reciprocal space) i0_reciprocal	14030000.0000
Solution quality estimate total_estimate	0.8969
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.264
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	228200.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Calmodulin
Molecular weight formula_weight	16687.4 kDa
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	1483

AEQLTEEQIAEFKEAFALFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLSLMARKMKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGEKLTDDEVDEMIREADIDGDGHINYEEFVRMMVSK

来源 Source

来源生物 organism	Paramecium tetraurelia
NCBI Class编号 ncbi_taxonomy_id	5888
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	LEAD (II) ION
Molecular weight formula_weight	207.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1n0ya_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

Domain ID domain_id	d1n0yb_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1n0yA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1n0yB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	100.936 Å
Unit-cell length b length_b	30.792 Å
Unit-cell length c length_c	113.084 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	53.000 Å
R factor r_factor	0.2144
R_work r_work	0.2134
R_free r_free	0.2228

fit	/app/data/saxs_computation/n0/1n0y/1n0y.fit
pddf	/app/data/pr_computation/n0/1n0y/1n0y.pr.out
profile	/app/data/saxs_computation/n0/1n0y/1n0y.dat

Crystal Structure of Pb-bound Calmodulin

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

Calmodulin

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