SAXSdb — 1d5t

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

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR

Bos taurus

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 1–431	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；295.5 K；ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 22.5K	Resolution 1.04 Å R-free 0.209

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 1D5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GND GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM Deposited 1996-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–447（447 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.81 Å R-free 0.275
1LV0 Crystal structure of the Rab effector guanine nucleotide dissociation inhibitor (GDI) in complex with a geranylgeranyl (GG) peptide Deposited 2002-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–447（447 aa）	Not recorded	SO4 SULFATE ION × 3 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；296 K；Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.00 Å R-free 0.249

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

View Construct and Data Evidence

UniProt name	GDIA_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–433； UniProt 1–431

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	1d5t
Deposition date deposition_date	1999-10-11
Structure title title	GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM
Keywords keywords	HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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	23.84 Å
Radius of gyration Rg (electron density) rg_electron	22.68 Å
Forward intensity I(0) i0	40144900.00
Molecular weight molecular_weight	48859.0 kDa
Excluded volume excluded_volume	61129 Å³
Envelope volume envelope_volume	72378 Å³
Hydration-shell volume shell_volume	26470 Å³
Envelope diameter envelope_diameter	80.4 Å
Shell Rg shell_rg	29.94 Å
Envelope Rg envelope_rg	22.91 Å
Shape Rg shape_rg	22.67 Å
Total Rg total_rg	23.59 Å
Total atoms total_atoms	3428
Residues n_residues	433
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	77.5 Å
Rg (real space) rg_real	23.75 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	4.0140e+07
I(0) uncertainty (real space) i0_real_error	5.8440e+05
Rg (reciprocal space) rg_reciprocal	23.77 Å
I(0) (reciprocal space) i0_reciprocal	40150000.0000
Solution quality estimate total_estimate	0.6525
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11040000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 0.999; Sysdev: 0.286; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR
Molecular weight formula_weight	48930.6 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	3827

HHMDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELYKRFQLLEGPPETMGRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYVPDRVRKAGQVIRIICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIASTTVETTDPEKEVEPALGLLEPIDQKFVAISDLYEPIDDGSESQVFCSCSYDATTHFETTCNDIKDIYKRMAGSAFDF

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	387

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d5ta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.3 — GDI-like N domain

Domain ID domain_id	d1d5ta2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.6 — GDI-like

CATH v4.4 (3 domains)

Domain ID domain_id	1d5tA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1d5tA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

Domain ID domain_id	1d5tA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

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8. Citations (1)

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Unit-cell length a length_a	89.290 Å
Unit-cell length b length_b	42.740 Å
Unit-cell length c length_c	61.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.040 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1730
R_work r_work	—
R_free r_free	0.2090

fit	/app/data/saxs_computation/d5/1d5t/1d5t.fit
pddf	/app/data/pr_computation/d5/1d5t/1d5t.pr.out
profile	/app/data/saxs_computation/d5/1d5t/1d5t.dat

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM

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

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR

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