SAXSdb — 1oot

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

Hypothetical 40.4 kDa protein in PES4-HIS2 intergenic region

Saccharomyces cerevisiae

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 314–373	Fragment：SH3 domain	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；295 K；70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 1.39 Å R-free 0.170

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 1OOT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SSH Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein in complex with a peptide Deposited 2004-03-24	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 A 315–373（59 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2.9M sodium malonate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.203

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

View Construct and Data Evidence

UniProt name	YFJ4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 314–373

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	1oot
Deposition date deposition_date	2003-03-04
Structure title title	Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution
Keywords keywords	SH3 DOMAIN, STURCTURAL GENOMICS, STRUCTURAL GENOMICS; STRUCTURAL GENOMICS
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	11.94 Å
Radius of gyration Rg (electron density) rg_electron	10.22 Å
Forward intensity I(0) i0	1015850.00
Molecular weight molecular_weight	6536.0 kDa
Excluded volume excluded_volume	8139 Å³
Envelope volume envelope_volume	8821 Å³
Hydration-shell volume shell_volume	7530 Å³
Envelope diameter envelope_diameter	34.1 Å
Shell Rg shell_rg	15.64 Å
Envelope Rg envelope_rg	10.67 Å
Shape Rg shape_rg	10.14 Å
Total Rg total_rg	11.94 Å
Total atoms total_atoms	459
Residues n_residues	58
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	36.7 Å
Rg (real space) rg_real	11.85 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	1.0160e+06
I(0) uncertainty (real space) i0_real_error	9.7710e+03
Rg (reciprocal space) rg_reciprocal	11.86 Å
I(0) (reciprocal space) i0_reciprocal	1016000.0000
Solution quality estimate total_estimate	0.8974
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.3 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	211400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.973

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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	Hypothetical 40.4 kDa protein in PES4-HIS2 intergenic region
Molecular weight formula_weight	6581.3 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	578

GSSPKAVALYSFAGEESGDLPFRKGDVITILKKSDSQNDWWTGRVNGREGIFPANYVELV

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1oota_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (1 domains)

Domain ID domain_id	1ootA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	39.930 Å
Unit-cell length b length_b	39.930 Å
Unit-cell length c length_c	69.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.390 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1340
R_work r_work	0.1321
R_free r_free	0.1705

fit	/app/data/saxs_computation/oo/1oot/1oot.fit
pddf	/app/data/pr_computation/oo/1oot/1oot.pr.out
profile	/app/data/saxs_computation/oo/1oot/1oot.dat

Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution

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

Hypothetical 40.4 kDa protein in PES4-HIS2 intergenic region

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