SAXSdb — 2q4u

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

Protein Zgc:100843

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 mmCIF provides none of the parsed experimental conditions	Resolution 2.10 Å R-free 0.242

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 2Q4U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BE4 X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843 Deposited 2005-10-21	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 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
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	2q4u
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, 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	20.81 Å
Radius of gyration Rg (electron density) rg_electron	20.57 Å
Forward intensity I(0) i0	3669130000.00
Molecular weight molecular_weight	508870.0 kDa
Excluded volume excluded_volume	631200 Å³
Envelope volume envelope_volume	60220 Å³
Hydration-shell volume shell_volume	23512 Å³
Envelope diameter envelope_diameter	76.4 Å
Shell Rg shell_rg	28.28 Å
Envelope Rg envelope_rg	21.58 Å
Shape Rg shape_rg	20.60 Å
Total Rg total_rg	20.59 Å
Total atoms total_atoms	35248
Residues n_residues	4160
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	68.7 Å
Rg (real space) rg_real	20.77 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	3.6690e+09
I(0) uncertainty (real space) i0_real_error	4.9900e+07
Rg (reciprocal space) rg_reciprocal	20.78 Å
I(0) (reciprocal space) i0_reciprocal	3669000000.0000
Solution quality estimate total_estimate	0.8902
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3498000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.998

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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	2q4uA01
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	2q4uA02
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	2q4uA03
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	44.170 Å
R factor r_factor	0.1540
R_work r_work	0.1540
R_free r_free	0.2420

Description description	Protein Zgc:100843
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	39088

Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843

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

Protein Zgc:100843

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/q4/2q4u/2q4u.fit
pddf	/app/data/pr_computation/q4/2q4u/2q4u.pr.out
profile	/app/data/saxs_computation/q4/2q4u/2q4u.dat