SAXSdb — 1ooj

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

Calmodulin CMD-1

Caenorhabditis elegans

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 1–149	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.7；295 K；PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K, RESERVOIR: MPD, PEG3350, DIOXANE, 5 MM CACL2, 50 MM CITRATE, PH 5.7, PROTEIN STOCK: 5 MG/ML IN 5 MM CACL2, 5 MM CACODYLATE, PH 6, DROPS: 5 MICROLITERS OF PROTEIN STOCK SOLUTION, 5 MICROLITERS OF RESERVOIR.	Resolution 2.11 Å R-free 0.271

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 1OOJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5H7D Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex Deposited 2016-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain E 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75) Chain F 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75) Chain G 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75) Chain H 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75)	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；296 K；0.1M HEPES pH 7.5, 20.7% PEG 300, 99mM calcium chloride	Resolution 2.57 Å R-free 0.241
5H7D Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex Deposited 2016-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain K 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75) Chain L 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75) Chain O 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75) Chain P 13–75（63 aa） Fragment：RESIDUES 104-156,157-219 (UNP RESIDUES 13-75)	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；296 K；0.1M HEPES pH 7.5, 20.7% PEG 300, 99mM calcium chloride	Resolution 2.57 Å R-free 0.241

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

View Construct and Data Evidence

UniProt name	CALM_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149

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	1ooj
Deposition date deposition_date	2003-03-03
Structure title title	Structural genomics of Caenorhabditis elegans : Calmodulin
Keywords keywords	;Structural genomics, Calmodulin, PSI, Protein Structure Initiative, Southeast Collaboratory for Structural Genomics, SECSG, 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	22.83 Å
Radius of gyration Rg (electron density) rg_electron	22.24 Å
Forward intensity I(0) i0	5179590.00
Molecular weight molecular_weight	16055.0 kDa
Excluded volume excluded_volume	19627 Å³
Envelope volume envelope_volume	26367 Å³
Hydration-shell volume shell_volume	10890 Å³
Envelope diameter envelope_diameter	69.9 Å
Shell Rg shell_rg	26.43 Å
Envelope Rg envelope_rg	21.50 Å
Shape Rg shape_rg	22.23 Å
Total Rg total_rg	22.83 Å
Total atoms total_atoms	1115
Residues n_residues	141
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	70.1 Å
Rg (real space) rg_real	23.02 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	5.1800e+06
I(0) uncertainty (real space) i0_real_error	6.6070e+04
Rg (reciprocal space) rg_reciprocal	22.98 Å
I(0) (reciprocal space) i0_reciprocal	5179000.0000
Solution quality estimate total_estimate	0.8094
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.1 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.975
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	283900.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.704; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 0.889

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Calmodulin CMD-1
Molecular weight formula_weight	16839.5 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	1206

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTTK

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 host_organism	Escherichia coli

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ooja_
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	1oojA01
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	1oojA02
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	103.394 Å
Unit-cell length b length_b	23.997 Å
Unit-cell length c length_c	60.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.14 °
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	2.110 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2230
R_work r_work	0.2120
R_free r_free	0.2710

fit	/app/data/saxs_computation/oo/1ooj/1ooj.fit
pddf	/app/data/pr_computation/oo/1ooj/1ooj.pr.out
profile	/app/data/saxs_computation/oo/1ooj/1ooj.dat

Structural genomics of Caenorhabditis elegans : Calmodulin

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

Calmodulin CMD-1

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