SAXSdb — 4a4p

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

CYTOHESIN1

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 63–248	Fragment：SEC7 DOMAIN, RESIDUES 63-248	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 3350 12%, AMMONIUM ACETATE 0.4M. GLYCEROL CRYO-PROTECTANT., pH 7	Resolution 2.00 Å R-free 0.222
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 63–248	Fragment：SEC7 DOMAIN, RESIDUES 63-248	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 3350 12%, AMMONIUM ACETATE 0.4M. GLYCEROL CRYO-PROTECTANT., pH 7	Resolution 2.00 Å R-free 0.222

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 4A4P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BC9 CYTOHESIN-1/B2-1 SEC7 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-05-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 58–256（199 aa） Fragment：SEC7 DOMAIN,	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 0.47 M；Pressure 1 NMR sample composition 20 MM NAPI, 150 MM (NH4)2SO4, 3MM DTT, 10% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–192； UniProt 63–248 Author chain B； PDBConstruct 7–192； UniProt 63–248

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	4a4p
Deposition date deposition_date	2011-10-19
Structure title title	crystal structure of the Sec7 domain from human cytohesin1
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	24.09 Å
Radius of gyration Rg (electron density) rg_electron	22.80 Å
Forward intensity I(0) i0	31796300.00
Molecular weight molecular_weight	43145.0 kDa
Excluded volume excluded_volume	54040 Å³
Envelope volume envelope_volume	66757 Å³
Hydration-shell volume shell_volume	24560 Å³
Envelope diameter envelope_diameter	76.7 Å
Shell Rg shell_rg	29.61 Å
Envelope Rg envelope_rg	22.86 Å
Shape Rg shape_rg	22.76 Å
Total Rg total_rg	23.82 Å
Total atoms total_atoms	3032
Residues n_residues	372
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	75.5 Å
Rg (real space) rg_real	23.98 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	3.1800e+07
I(0) uncertainty (real space) i0_real_error	4.1800e+05
Rg (reciprocal space) rg_reciprocal	24.01 Å
I(0) (reciprocal space) i0_reciprocal	31800000.0000
Solution quality estimate total_estimate	0.9078
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.185
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5323000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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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	CYTOHESIN1
Molecular weight formula_weight	22355.5 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	3410

HHHHHHNKQVAMGRKKFNMDPKKGIQFLIENDLLKNTCEDIAQFLYKGEGLNKTAIGDYLGERDEFNIQVLHAFVELHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNNGVFQSTDTCYVLSFAIIMLNTSLHNPNVKDKPTVERFIAMNRGINDGGDLPEELLRNLYESIKNEPFKIPE

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	GLYCEROL
Molecular weight formula_weight	92.1 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	378

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4a4pa_
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.118.3.1 — Sec7 domain

Domain ID domain_id	d4a4pb_
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.118.3.1 — Sec7 domain

CATH v4.4 (4 domains)

Domain ID domain_id	4a4pA01
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	4a4pA02
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	4a4pB01
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	4a4pB02
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	47.090 Å
Unit-cell length b length_b	80.280 Å
Unit-cell length c length_c	51.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.17 °
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	2.000 Å
Low-resolution limit resolution_low	32.030 Å
R factor r_factor	0.1762
R_work r_work	0.1737
R_free r_free	0.2222

fit	/app/data/saxs_computation/a4/4a4p/4a4p.fit
pddf	/app/data/pr_computation/a4/4a4p/4a4p.pr.out
profile	/app/data/saxs_computation/a4/4a4p/4a4p.dat

crystal structure of the Sec7 domain from human cytohesin1

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

CYTOHESIN1

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