SAXSdb — 3ltl

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

Brefeldin A-inhibited guanine nucleotide-exchange protein 1

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 691–889	Fragment：Sec7 domain	CA CALCIUM ION × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；293 K；30% PEG 3350, 0.2M sodium acetate, 0.2M tris pH 7.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.20 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 691–889	Fragment：Sec7 domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；293 K；30% PEG 3350, 0.2M sodium acetate, 0.2M tris pH 7.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.20 Å R-free 0.236

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 3LTL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EE5 Structure of human ARL1 in complex with the DCB domain of BIG1 Deposited 2015-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–229（229 aa）	Mutation：delta-52-70 Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 14 GOL GLYCEROL × 2 CL CHLORIDE ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 8K/PEG 1k 10% Sodium Acetate 0.1-0.2mM Tris pH8.5 glacial acetic 0.100mM	Resolution 2.28 Å R-free 0.259
5J5C Crystal structure of ARL1-GTP and DCB domain of BIG1 complex Deposited 2016-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–224（224 aa） Fragment：DCB domain, UNP residues 1-224	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；289 K；0.2M lithium sulfate, 0.1M sodium citrate tribasic, 0.1M Tris-HCl pH 9.1, and 27% (w/v) polyethylene glycol 3350	Resolution 3.40 Å R-free 0.258

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

View Construct and Data Evidence

UniProt name	BIG1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–209； UniProt 691–889 Author chain B； PDBConstruct 11–209； UniProt 691–889

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	3ltl
Deposition date deposition_date	2010-02-16
Structure title title	Crystal structure of human BIG1 Sec7 domain
Keywords keywords	all alpha, Guanine-nucleotide releasing factor, SIGNALING PROTEIN; SIGNALING PROTEIN
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	25.95 Å
Radius of gyration Rg (electron density) rg_electron	24.93 Å
Forward intensity I(0) i0	31481900.00
Molecular weight molecular_weight	43530.0 kDa
Excluded volume excluded_volume	54553 Å³
Envelope volume envelope_volume	68681 Å³
Hydration-shell volume shell_volume	22977 Å³
Envelope diameter envelope_diameter	81.0 Å
Shell Rg shell_rg	32.05 Å
Envelope Rg envelope_rg	24.51 Å
Shape Rg shape_rg	24.93 Å
Total Rg total_rg	25.76 Å
Total atoms total_atoms	3055
Residues n_residues	377
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	77.2 Å
Rg (real space) rg_real	25.86 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.1480e+07
I(0) uncertainty (real space) i0_real_error	4.1550e+05
Rg (reciprocal space) rg_reciprocal	25.89 Å
I(0) (reciprocal space) i0_reciprocal	31480000.0000
Solution quality estimate total_estimate	0.9152
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.099
Kurtosis Kurtosis kurtosis	-0.760
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5488000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Brefeldin A-inhibited guanine nucleotide-exchange protein 1
Molecular weight formula_weight	24391.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3142

MGHHHHHHGTQFEVLKQQKEIIEQGIDLFNKKPKRGIQYLQEQGMLGTTPEDIAQFLHQEERLDSTQVGEFLGDNDKFNKEVMYAYVDQHDFSGKDFVSALRMFLEGFRLPGEAQKIDRLMEKFAARYLECNQGQTLFASADTAYVLAYSIIMLTTDLHSPQVKNKMTKEQYIKMNRGINDSKDLPEEYLSAIYNEIAGKKISMKETKETG

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ltla_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.3 — Sec7 domain
Family Family family	a.118.3.0 — automated matches

Domain ID domain_id	d3ltlb_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.3 — Sec7 domain
Family Family family	a.118.3.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3ltlA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ltlA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1000 — Arf Nucleotide-binding Site Opener; domain 2
Homologous superfamily homologous superfamily	11 — Arf Nucleotide-binding Site Opener,domain 2

Domain ID domain_id	3ltlB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ltlB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1000 — Arf Nucleotide-binding Site Opener; domain 2
Homologous superfamily homologous superfamily	11 — Arf Nucleotide-binding Site Opener,domain 2

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8. Citations (1)

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Unit-cell length a length_a	64.451 Å
Unit-cell length b length_b	36.867 Å
Unit-cell length c length_c	85.848 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	22.605 Å
R factor r_factor	0.1785
R_work r_work	0.1753
R_free r_free	0.2365

fit	/app/data/saxs_computation/lt/3ltl/3ltl.fit
pddf	/app/data/pr_computation/lt/3ltl/3ltl.pr.out
profile	/app/data/saxs_computation/lt/3ltl/3ltl.dat

Crystal structure of human BIG1 Sec7 domain

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

Brefeldin A-inhibited guanine nucleotide-exchange protein 1

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