SAXSdb — 1d4b

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

HUMAN CELL DEATH-INDUCING EFFECTOR B

Homo sapiens

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 1–116	Fragment：N-TERMINAL DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure 1 NMR sample composition：0.5MM CIDE-N OF CIDE-B	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CIDEB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 1–116

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	1d4b
Deposition date deposition_date	1999-10-02
Structure title title	CIDE-N DOMAIN OF HUMAN CIDE-B
Keywords keywords	ALPHA/BETA ROLL, APOPTOSIS; APOPTOSIS
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.72 Å
Radius of gyration Rg (electron density) rg_electron	32.00 Å
Forward intensity I(0) i0	641348000.00
Molecular weight molecular_weight	205900.0 kDa
Excluded volume excluded_volume	255510 Å³
Envelope volume envelope_volume	190490 Å³
Hydration-shell volume shell_volume	37902 Å³
Envelope diameter envelope_diameter	159.5 Å
Shell Rg shell_rg	42.28 Å
Envelope Rg envelope_rg	51.07 Å
Shape Rg shape_rg	31.93 Å
Total Rg total_rg	32.53 Å
Total atoms total_atoms	28770
Residues n_residues	1830
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	61.4 Å
Rg (real space) rg_real	21.17 Å
Rg uncertainty (real space) rg_real_error	0.13 Å
I(0) (real space) i0_real	5.2480e+08
I(0) uncertainty (real space) i0_real_error	5.8990e+06
Rg (reciprocal space) rg_reciprocal	31.64 Å
I(0) (reciprocal space) i0_reciprocal	641000000.0000
Solution quality estimate total_estimate	0.5646
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.465
Kurtosis Kurtosis kurtosis	-0.646
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	6.4130
Highest regularization parameter α highest_alpha	1176000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.047; Oscil: 0.891; Stabil: 0.943; Sysdev: 0.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d4ba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.2 — CAD & PB1 domains
Family Family family	d.15.2.1 — CAD domain

Domain ID domain_id	d1d4ba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1d4bA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	HUMAN CELL DEATH-INDUCING EFFECTOR B
Molecular weight formula_weight	13748.5 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	28770

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

CIDE-N DOMAIN OF HUMAN CIDE-B

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

HUMAN CELL DEATH-INDUCING EFFECTOR B

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/d4/1d4b/1d4b.fit
pddf	/app/data/pr_computation/d4/1d4b/1d4b.pr.out
profile	/app/data/saxs_computation/d4/1d4b/1d4b.dat