SAXSdb — 5e1n

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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 2–149	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

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 5E1N	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 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 1–148（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 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）	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
1N0Y Crystal Structure of Pb-bound Calmodulin Deposited 2002-10-15	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 1–148（148 aa）	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
1N0Y Crystal Structure of Pb-bound Calmodulin Deposited 2002-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–148（148 aa）	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
1OSA CRYSTAL STRUCTURE OF RECOMBINANT PARAMECIUM TETRAURELIA CALMODULIN AT 1.68 ANGSTROMS RESOLUTION Deposited 1993-08-11	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 1–148（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 mutation/modification 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 mutation/modification 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 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
5E1P Ca(2+)-Calmodulin from Paramecium tetraurelia qFit disorder model Deposited 2015-09-29	Different mutation/modification 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 9 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 2–149

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	5e1n
Deposition date deposition_date	2015-09-29
Structure title title	Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia qFit disorder model
Keywords keywords	calcium signaling, EF hand, calcium binding, 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	23.39 Å
Radius of gyration Rg (electron density) rg_electron	23.12 Å
Forward intensity I(0) i0	1894990.00
Molecular weight molecular_weight	8923.0 kDa
Excluded volume excluded_volume	10702 Å³
Envelope volume envelope_volume	19488 Å³
Hydration-shell volume shell_volume	8198 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	25.97 Å
Envelope Rg envelope_rg	21.10 Å
Shape Rg shape_rg	23.21 Å
Total Rg total_rg	23.39 Å
Total atoms total_atoms	1150
Residues n_residues	81
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	69.6 Å
Rg (real space) rg_real	23.54 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.8950e+06
I(0) uncertainty (real space) i0_real_error	2.8940e+04
Rg (reciprocal space) rg_reciprocal	23.51 Å
I(0) (reciprocal space) i0_reciprocal	1895000.0000
Solution quality estimate total_estimate	0.7512
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	15.0 Å
Skewness Skewness skewness	0.116
Kurtosis Kurtosis kurtosis	-1.178
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	92090.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.482; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.348; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Calmodulin
Molecular weight formula_weight	17062.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6066

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	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5e1na_
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

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8. Citations (1)

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Unit-cell length a length_a	25.036 Å
Unit-cell length b length_b	29.409 Å
Unit-cell length c length_c	52.793 Å
Unit-cell angle α angle_alpha	89.45 °
Unit-cell angle β angle_beta	86.29 °
Unit-cell angle γ angle_gamma	82.39 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.000 Å
Low-resolution limit resolution_low	24.760 Å
R factor r_factor	0.1350
R_work r_work	0.1340
R_free r_free	0.1500

fit	/app/data/saxs_computation/e1/5e1n/5e1n.fit
pddf	/app/data/pr_computation/e1/5e1n/5e1n.pr.out
profile	/app/data/saxs_computation/e1/5e1n/5e1n.dat

Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia qFit disorder model

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