SAXSdb — 1f3c

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

DYNEIN

Rattus norvegicus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–89 Chain B； UniProt 1–89	Fragment：8KDA LIGHT CHAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；303 K NMR sample composition：1.5mM DLC8; 100mM phosphate buffer NA; 99.99% D2O \| 99.99% D2O NMR sample composition：1.5mM DLC8 U-15N;100mM phosphate buffer NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：1.5mM DLC8 U-15N,13C;100mM phosphate buffer NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	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.

Other PDB	Difference from Current Entry 1F3C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F95 SOLUTION STRUCTURE OF DYNEIN LIGHT CHAIN 8 (DLC8) AND BIM PEPTIDE COMPLEX Deposited 2000-07-07	Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa） Fragment：8KDA LIGHT CHAIN Chain B 1–89（89 aa） Fragment：8KDA LIGHT CHAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 1.5mM DLC8/Bim peptide complex 15N; 100mM phosphate buffer; 10mM DTT; 90% H2O and 10% D2O \| 90% H2O and 10% D2O NMR sample composition 1.5mM DLC8/Bim peptide complex 15N,13C; 100mM phosphate buffer; 10mM DTT; 90% H2O and 10% D2O \| 90% H2O and 10% D2O NMR sample composition 1.5mM DLC8/Bim peptide complex ; 100mM phosphate buffer; 10mM DTT; 99.9% D2O \| 99.9% D2O	Resolution not provided
1F96 SOLUTION STRUCTURE OF DYNEIN LIGHT CHAIN 8 (DLC8) AND NNOS PEPTIDE COMPLEX Deposited 2000-07-07	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa） Fragment：DLC8 BINDING REGION Chain B 1–89（89 aa） Fragment：DLC8 BINDING REGION	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 1.5mM DLC8/nNOS ppetide complex 15N; 100mM phosphate buffer; 10mM DTT; 90%H2O and 10% D2O \| 90%H2O and 10% D2O NMR sample composition 1.5mM DLC8/nNOS ppetide complex 15N,13C; 100mM phosphate buffer; 10mM DTT; 90%H2O and 10% D2O \| 90%H2O and 10% D2O NMR sample composition 1.5mM DLC8/nNOS ppetide complex ; 100mM phosphate buffer; 10mM DTT; 99.9% D2O \| 99.9% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	DYL1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 1–89 Author chain B； PDBConstruct 1–89； UniProt 1–89

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	1f3c
Deposition date deposition_date	2000-06-02
Structure title title	REFINED SOLUTION STRUCTURE OF 8KDA DYNEIN LIGHT CHAIN (DLC8)
Keywords keywords	dynein, light chain, DLC8, microtubules, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN
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	16.18 Å
Radius of gyration Rg (electron density) rg_electron	15.70 Å
Forward intensity I(0) i0	2332440000.00
Molecular weight molecular_weight	414640.0 kDa
Excluded volume excluded_volume	519400 Å³
Envelope volume envelope_volume	40648 Å³
Hydration-shell volume shell_volume	18641 Å³
Envelope diameter envelope_diameter	66.8 Å
Shell Rg shell_rg	24.64 Å
Envelope Rg envelope_rg	18.80 Å
Shape Rg shape_rg	15.60 Å
Total Rg total_rg	16.17 Å
Total atoms total_atoms	57840
Residues n_residues	3560
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	56.2 Å
Rg (real space) rg_real	16.16 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.3320e+09
I(0) uncertainty (real space) i0_real_error	2.8370e+07
Rg (reciprocal space) rg_reciprocal	16.16 Å
I(0) (reciprocal space) i0_reciprocal	2332000000.0000
Solution quality estimate total_estimate	0.6328
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.195
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1159000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 0.998; Sysdev: 0.353; Positv: 1.000; Valcen: 0.985; 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1f3ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.39 — DLC
Superfamily Superfamily superfamily	d.39.1 — DLC
Family Family family	d.39.1.1 — DLC

Domain ID domain_id	d1f3cb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.39 — DLC
Superfamily Superfamily superfamily	d.39.1 — DLC
Family Family family	d.39.1.1 — DLC

CATH v4.4 (2 domains)

Domain ID domain_id	1f3cA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

Domain ID domain_id	1f3cB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

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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	DYNEIN
Molecular weight formula_weight	10381.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	57840

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

REFINED SOLUTION STRUCTURE OF 8KDA DYNEIN LIGHT CHAIN (DLC8)

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

DYNEIN

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/f3/1f3c/1f3c.fit
pddf	/app/data/pr_computation/f3/1f3c/1f3c.pr.out
profile	/app/data/saxs_computation/f3/1f3c/1f3c.dat