SAXSdb — 2o60

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

Calmodulin

Gallus gallus

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–148	Not recorded	Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase × 1 （Q9Z0J4） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；20% PEG 4000, 0.2 M sodium acetate, 0.1 M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.55 Å R-free 0.244

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 2O60	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AHR CALMODULIN MUTANT WITH A TWO RESIDUE DELETION IN THE CENTRAL HELIX Deposited 1997-04-10	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Mutation：DEL(T79), DEL(D80)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.25；28-33% MPD, 15% ETHANOL, 5MM CACL, 20MM NA ACETATE, PH 4.25	Resolution 1.80 Å
1UP5 Chicken Calmodulin Deposited 2003-09-27	Different construct Different mutation/modification Different oligomeric state 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 × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；HANGING DROPS 12UL CAM 12MG/ML + 8UL PRECIPITANT, SEEDED 10MM NAOAC, PH 4.0, 30% MPD, 15% ISOPROPANOL	Resolution 1.90 Å R-free 0.259
1UP5 Chicken Calmodulin Deposited 2003-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–149（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 4；HANGING DROPS 12UL CAM 12MG/ML + 8UL PRECIPITANT, SEEDED 10MM NAOAC, PH 4.0, 30% MPD, 15% ISOPROPANOL	Resolution 1.90 Å R-free 0.259
2BCX Crystal structure of calmodulin in complex with a ryanodine receptor peptide Deposited 2005-10-19	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 4.7；293 K；23% PEG 4000, 0.1 M sodium acetate, 5 mM DTT, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.249
2BKI Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure Deposited 2005-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–148（148 aa） Chain D 1–148（148 aa）	Not recorded	SO4 SULFATE ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 8-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL	Resolution 2.90 Å R-free 0.304
2KZ2 Calmodulin, C-terminal domain, F92E mutant Deposited 2010-06-10	Different construct Different mutation/modification Different oligomeric state 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 77–149（73 aa） Fragment：UNP residues 77-149	Mutation：F92E	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 6.9；293 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] cCaMF92E-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] cCaMF92E-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M3S Calmodulin, i85l, f92e, h107i, l112r, a128t, m144r mutant Deposited 2013-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–149（149 aa） Fragment：UNP residues 1-149	Mutation：I85L, F92E, H107I, L107I, A128T, M144R	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.91；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.68 mM [U-100% 13C; U-100% 15N] protein_1, 0.005 % DSS, 20 mM HEPES, 100 mM sodium chloride, 10 mM calcium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 15N] protein_1, 0.005 % DSS, 20 mM HEPES, 100 mM sodium chloride, 10 mM calcium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2O5G Calmodulin-smooth muscle light chain kinase peptide complex Deposited 2006-12-05	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 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；30% PEG 400, 0.2 M sodium acetate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.08 Å R-free 0.165
2VB6 Myosin VI (MD-insert2-CaM, Delta Insert1) Post-rigor state (crystal form 2) Deposited 2007-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 10% PEG 8000, 50MM GLYCINE PH 9.5, 6% MPD	Resolution 2.30 Å R-free 0.253
3GOF Calmodulin bound to peptide from macrophage nitric oxide synthase Deposited 2009-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.45 Å R-free 0.208
3GOF Calmodulin bound to peptide from macrophage nitric oxide synthase Deposited 2009-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.45 Å R-free 0.208
3GP2 Calmodulin bound to peptide from calmodulin kinase II (CaMKII) Deposited 2009-03-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–148（147 aa）	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.46 Å R-free 0.192
3GP2 Calmodulin bound to peptide from calmodulin kinase II (CaMKII) Deposited 2009-03-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–148（147 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.46 Å R-free 0.192
5HIT Crystal Structure Analysis of Ca2+-calmodulin and a C-terminal EAG1 channel fragment Deposited 2016-01-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–148（147 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；di-ammonium citrate, PEG 3350	Resolution 2.85 Å R-free 0.268
6BNV CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state, backbone-averaged with side chains truncated to alanine Deposited 2017-11-17	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 × 20 PDB declaration: eicosameric	Chain O 4–148（145 aa） Chain P 4–148（145 aa） Chain Q 4–148（145 aa） Chain R 4–148（145 aa） Chain S 4–148（145 aa） Chain T 4–148（145 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer was filtered through 0.44 um filter and degassed. cryo-EM vitrification conditions Cryogen ETHANE；Sample was applied to a glow-discharged holey carbon grid. 3 uL actin was incubated for 60 seconds. 3 uL of myosin VI was added and incubated for 60 seconds. 3 uL solution was removed. An additional 3 uL of myosin VI was applied. After 60 seconds, 3 uL solution was removed, and the grid was blotted for 3 seconds from the backside with filter paper.	Resolution 4.60 Å

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

View Construct and Data Evidence

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

Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase

OrganismNot specified

UniProt Q9Z0J4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 725–747	Non-standard monomer：Yes (specific site not provided by mmCIF)	Calmodulin × 1 （P62149） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；20% PEG 4000, 0.2 M sodium acetate, 0.1 M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.55 Å R-free 0.244

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 2O60	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMI STRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE Deposited 1999-05-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 225–237（13 aa） Fragment：RESIDUE 225-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；pH 8.4	Resolution 2.50 Å R-free 0.283
1CMI STRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE Deposited 1999-05-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 225–237（13 aa） Fragment：RESIDUE 225-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；pH 8.4	Resolution 2.50 Å R-free 0.283

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

View Construct and Data Evidence

UniProt name	NOS1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–23； UniProt 725–747

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	2o60
Deposition date deposition_date	2006-12-06
Structure title title	Calmodulin bound to peptide from neuronal nitric oxide synthase
Keywords keywords	protein-peptide complex, 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	17.42 Å
Radius of gyration Rg (electron density) rg_electron	15.96 Å
Forward intensity I(0) i0	7374740.00
Molecular weight molecular_weight	18982.0 kDa
Excluded volume excluded_volume	23382 Å³
Envelope volume envelope_volume	27508 Å³
Hydration-shell volume shell_volume	14730 Å³
Envelope diameter envelope_diameter	53.2 Å
Shell Rg shell_rg	21.53 Å
Envelope Rg envelope_rg	16.06 Å
Shape Rg shape_rg	15.98 Å
Total Rg total_rg	16.88 Å
Total atoms total_atoms	1320
Residues n_residues	168
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	54.4 Å
Rg (real space) rg_real	17.32 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	7.3750e+06
I(0) uncertainty (real space) i0_real_error	8.0630e+04
Rg (reciprocal space) rg_reciprocal	17.33 Å
I(0) (reciprocal space) i0_reciprocal	7375000.0000
Solution quality estimate total_estimate	0.9027
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.7 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	896100.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.990

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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	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1513

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase
Molecular weight formula_weight	2583.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KRRAIGFKKLAEAVKFSAKLMGQX

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	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	165

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2o60a_
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	2o60A00
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	67.126 Å
Unit-cell length b length_b	32.930 Å
Unit-cell length c length_c	73.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	74.540 Å
R factor r_factor	0.2038
R_work r_work	0.2016
R_free r_free	0.2437

fit	/app/data/saxs_computation/o6/2o60/2o60.fit
pddf	/app/data/pr_computation/o6/2o60/2o60.pr.out
profile	/app/data/saxs_computation/o6/2o60/2o60.dat

Calmodulin bound to peptide from neuronal nitric oxide synthase

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

Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)