SAXSdb — 1zuk

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

Myosin tail region-interacting protein MTI1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–68 Chain B； UniProt 1–68	Fragment：SH3 domain	Proline-rich protein LAS17 × 1 （Q12446） CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.226

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 1ZUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TG0 0.97-A structure of the SH3 domain of bbc1 Deposited 2004-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–68（68 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；3.2M ammonium sulfate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 0.97 Å R-free 0.193
1WDX Yeast BBC1 SH3 domain, triclinic crystal form Deposited 2004-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–68（68 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.326
1WDX Yeast BBC1 SH3 domain, triclinic crystal form Deposited 2004-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–68（68 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.326
1WDX Yeast BBC1 SH3 domain, triclinic crystal form Deposited 2004-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–68（68 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.326
1WDX Yeast BBC1 SH3 domain, triclinic crystal form Deposited 2004-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–68（68 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.326
2DYF Solution structure of the first WW domain of FBP11 / HYPA (FBP11 WW1) complexed with a PL (PPLP) motif peptide ligand Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 796–802（7 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；283 K；Ionic strength (raw mmCIF value) 0.3；Pressure 1 NMR sample composition 1.5MM FBP11 WW1 U-15N, 13C 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.5MM FBP11 WW1 U- 15N, 13C; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.5MM FBP11 WW1 U-15N; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O	Resolution not provided

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BBC1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–68； UniProt 1–68 Author chain B； PDBConstruct 1–68； UniProt 1–68

Proline-rich protein LAS17

OrganismNot specified

UniProt Q12446

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 350–360	Fragment：PxxP motif	Myosin tail region-interacting protein MTI1 × 2 （P47068） CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.226

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	LAS17_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–11； UniProt 350–360

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	1zuk
Deposition date deposition_date	2005-05-31
Structure title title	Yeast BBC1 Sh3 domain complexed with a peptide from Las17
Keywords keywords	SH3 domain, PxxP peptide, CONTRACTILE PROTEIN; CONTRACTILE 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	17.61 Å
Radius of gyration Rg (electron density) rg_electron	16.54 Å
Forward intensity I(0) i0	4940790.00
Molecular weight molecular_weight	16291.0 kDa
Excluded volume excluded_volume	20377 Å³
Envelope volume envelope_volume	24020 Å³
Hydration-shell volume shell_volume	12889 Å³
Envelope diameter envelope_diameter	59.7 Å
Shell Rg shell_rg	21.51 Å
Envelope Rg envelope_rg	16.96 Å
Shape Rg shape_rg	16.49 Å
Total Rg total_rg	17.61 Å
Total atoms total_atoms	1157
Residues n_residues	141
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	60.4 Å
Rg (real space) rg_real	17.63 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	4.9410e+06
I(0) uncertainty (real space) i0_real_error	5.5330e+04
Rg (reciprocal space) rg_reciprocal	17.63 Å
I(0) (reciprocal space) i0_reciprocal	4941000.0000
Solution quality estimate total_estimate	0.8664
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.377
Kurtosis Kurtosis kurtosis	-0.282
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1388000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Myosin tail region-interacting protein MTI1
Molecular weight formula_weight	7821.5 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	1354

MSEPEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAVQG

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 polymer

Description description	Proline-rich protein LAS17
Molecular weight formula_weight	1181.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

RGPAPPPPPHR

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	179

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1zukA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	1zukB00
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	51.770 Å
Unit-cell length b length_b	78.500 Å
Unit-cell length c length_c	35.460 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1764
R_work r_work	0.1739
R_free r_free	0.2260

fit	/app/data/saxs_computation/zu/1zuk/1zuk.fit
pddf	/app/data/pr_computation/zu/1zuk/1zuk.pr.out
profile	/app/data/saxs_computation/zu/1zuk/1zuk.dat

Yeast BBC1 Sh3 domain complexed with a peptide from Las17

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

Myosin tail region-interacting protein MTI1

State in the Current Structure

Other States of the Same Protein in the Database

Proline-rich protein LAS17

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)