SAXSdb — 3if7

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

Calmodulin

OrganismNot specified

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	Not recorded	CA CALCIUM ION × 4 SPU 2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；50mM sodium cacodylate, 10mM CaCl2, 10mM MgCl2, 28% PEG 8000: Mixed with 10mM lipid in methanol solution and 1mM protein solution, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.238

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 3IF7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A29 CALMODULIN COMPLEXED WITH TRIFLUOPERAZINE (1:2 COMPLEX) Deposited 1998-01-19	Different construct 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 TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED BY SITTING DROP TECHNIQUE IN THE COLD ROOM (8 DEGREES C +/- 2 DEGREES C) BY MIXING 4 MICROLITERS OF 1 MM PROTEIN CONTAINING 1.2-1.5 MM TFP IN 5 MM CACL2 WITH 4 MICROLITERS OF THE RESERVOIR SOLUTION (1 ML 10 MM SODIUM CACODYLATE/HCL BUFFER, PH 5.2-5.6 WITH 10 MM CACL2, 25-30 % (W/V) POLYETHYLENE GLYCOL 6000), CRYSTAL GROWTH TOOK 2-3 WEEKS., pH 5.0	Resolution 2.74 Å R-free 0.265
1AK8 NMR SOLUTION STRUCTURE OF CERIUM-LOADED CALMODULIN AMINO-TERMINAL DOMAIN (CE2-TR1C), 23 STRUCTURES Deposited 1997-05-29	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–75（75 aa） Fragment：N-TERMINAL DOMAIN, TR1C	Not recorded	CE CERIUM (III) ION × 2	SOLUTION NMR NMR measurement conditions pH 6；298 K	Resolution not provided
1CDM MODULATION OF CALMODULIN PLASTICITY IN MOLECULAR RECOGNITION ON THE BASIS OF X-RAY STRUCTURES Deposited 1993-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 4–147（144 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1CMF NMR SOLUTION STRUCTURE OF APO CALMODULIN CARBOXY-TERMINAL DOMAIN Deposited 1995-07-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 76–148（73 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CMG NMR SOLUTION STRUCTURE OF CALCIUM-LOADED CALMODULIN CARBOXY-TERMINAL DOMAIN Deposited 1995-07-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 76–148（73 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1FW4 CRYSTAL STRUCTURE OF E. COLI FRAGMENT TR2C FROM CALMODULIN TO 1.7 A RESOLUTION Deposited 2000-09-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–148（71 aa） Fragment：C-TERMINAL DOMAIN (RESIDUES 78-148)	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG 4000, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.220
1LIN CALMODULIN COMPLEXED WITH TRIFLUOPERAZINE (1:4 COMPLEX) Deposited 1995-10-11	Different construct 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 TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1PRW Crystal structure of bovine brain Ca++ calmodulin in a compact form Deposited 2003-06-20	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）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；296 K；PEG 6000, sodium acetate, glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.70 Å R-free 0.230
1XA5 Structure of Calmodulin in complex with KAR-2, a bis-indol alkaloid Deposited 2004-08-25	Different construct 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 KAR 3"-(BETA-CHLOROETHYL)-2",4"-DIOXO-3, 5"-SPIRO-OXAZOLIDINO-4-DEACETOXY-VINBLASTINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；279 K；CaCl2, MgCl2, cacodylate, PEG 8000, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.12 Å R-free 0.261
2F2O Structure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode Deposited 2005-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–148（149 aa） Chain B 0–148（149 aa）	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.17 Å R-free 0.289
2F2O Structure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode Deposited 2005-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 0–148（149 aa） Chain B 0–148（149 aa）	Not recorded	CA CALCIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.17 Å R-free 0.289
2F2P Structure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode Deposited 2005-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–148（149 aa） Chain B 0–148（149 aa）	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.297
2F2P Structure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode Deposited 2005-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 0–148（149 aa） Chain B 0–148（149 aa）	Not recorded	CA CALCIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.297
2FOT Crystal structure of the complex between calmodulin and alphaII-spectrin Deposited 2006-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；50mM Tris,pH 8.00, 30% PEG 8000, 0.1M ammonium-sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.45 Å R-free 0.269
6O20 Cryo-EM structure of TRPV5 with calmodulin bound Deposited 2019-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM_BOVIN
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	3if7
Deposition date deposition_date	2009-07-24
Structure title title	Structure of Calmodulin complexed with its first endogenous inhibitor, sphingosylphosphorylcholine
Keywords keywords	EF-hand, phospholipid, calcium binding protein, Isopeptide bond, Methylation, Phosphoprotein; CALCIUM 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	16.40 Å
Radius of gyration Rg (electron density) rg_electron	14.81 Å
Forward intensity I(0) i0	5684860.00
Molecular weight molecular_weight	16845.0 kDa
Excluded volume excluded_volume	20903 Å³
Envelope volume envelope_volume	23542 Å³
Hydration-shell volume shell_volume	13532 Å³
Envelope diameter envelope_diameter	48.1 Å
Shell Rg shell_rg	20.49 Å
Envelope Rg envelope_rg	14.93 Å
Shape Rg shape_rg	14.86 Å
Total Rg total_rg	15.73 Å
Total atoms total_atoms	1167
Residues n_residues	142
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	50.4 Å
Rg (real space) rg_real	16.28 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	5.6850e+06
I(0) uncertainty (real space) i0_real_error	6.5170e+04
Rg (reciprocal space) rg_reciprocal	16.29 Å
I(0) (reciprocal space) i0_reciprocal	5685000.0000
Solution quality estimate total_estimate	0.8987
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.069
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	671500.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.972

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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	16721.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1256

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium
Molecular weight formula_weight	465.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	79

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3if7a_
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 (1 domains)

Domain ID domain_id	3if7A00
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	39.669 Å
Unit-cell length b length_b	39.669 Å
Unit-cell length c length_c	170.340 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	29.390 Å
R factor r_factor	0.1946
R_work r_work	0.1923
R_free r_free	0.2382

fit	/app/data/saxs_computation/if/3if7/3if7.fit
pddf	/app/data/pr_computation/if/3if7/3if7.pr.out
profile	/app/data/saxs_computation/if/3if7/3if7.dat

Structure of Calmodulin complexed with its first endogenous inhibitor, sphingosylphosphorylcholine

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