SAXSdb — 2be4

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

hypothetical protein LOC449832

Danio rerio

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 2–272	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；10 MG/ML PROTEIN, 26% PEG 2K, 0.100 M BTP, pH 9.0, vapor diffusion, hanging drop, temperature 277K	Resolution 2.10 Å R-free 0.253

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 2BE4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Q4U Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843 Deposited 2007-05-31	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–272（271 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.242
6JLH Structure of SCGN in complex with a Snap25 peptide Deposited 2019-03-05	Different construct Different mutation/modification 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 7–267（261 aa） Chain C 7–267（261 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 12 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M glycocine, 0.1 M Tris Bicine pH 8.5, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350	Resolution 2.37 Å R-free 0.237

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

View Construct and Data Evidence

UniProt name	Q5XJX1_BRARE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–272； UniProt 2–272

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	2be4
Deposition date deposition_date	2005-10-21
Structure title title	X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843
Keywords keywords	;Dr.36843, BC083168, CALICIUM BINDING, EF-HAND SUPERFAMILY, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS, CESG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	21.60 Å
Radius of gyration Rg (electron density) rg_electron	20.59 Å
Forward intensity I(0) i0	18292800.00
Molecular weight molecular_weight	31804.0 kDa
Excluded volume excluded_volume	39450 Å³
Envelope volume envelope_volume	48593 Å³
Hydration-shell volume shell_volume	20026 Å³
Envelope diameter envelope_diameter	74.7 Å
Shell Rg shell_rg	26.78 Å
Envelope Rg envelope_rg	20.74 Å
Shape Rg shape_rg	20.62 Å
Total Rg total_rg	21.39 Å
Total atoms total_atoms	2203
Residues n_residues	260
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	73.4 Å
Rg (real space) rg_real	21.55 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.8290e+07
I(0) uncertainty (real space) i0_real_error	2.3960e+05
Rg (reciprocal space) rg_reciprocal	21.56 Å
I(0) (reciprocal space) i0_reciprocal	18290000.0000
Solution quality estimate total_estimate	0.8763
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.272
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5694000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2be4A01
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	2be4A02
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	2be4A03
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	47.884 Å
Unit-cell length b length_b	52.748 Å
Unit-cell length c length_c	114.364 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	57.166 Å
R factor r_factor	0.1794
R_work r_work	0.1755
R_free r_free	0.2529

Description description	hypothetical protein LOC449832
Molecular weight formula_weight	32050.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2445

X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843

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

hypothetical protein LOC449832

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Danio rerio
通用名 common_name	zebrafish
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

fit	/app/data/saxs_computation/be/2be4/2be4.fit
pddf	/app/data/pr_computation/be/2be4/2be4.pr.out
profile	/app/data/saxs_computation/be/2be4/2be4.dat