SAXSdb — 1z9z

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

Cytoskeleton assembly control protein SLA1

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 357–413	Fragment：SH3 domain 3	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.95 Å R-free 0.229
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 357–413	Fragment：SH3 domain 3	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.95 Å R-free 0.229
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 357–413 Chain B； UniProt 357–413	Fragment：SH3 domain 3	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.95 Å R-free 0.229
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 357–413 Chain B； UniProt 357–413	Fragment：SH3 domain 3	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.95 Å R-free 0.229
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 357–413	Fragment：SH3 domain 3	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.95 Å R-free 0.229

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 1Z9Z	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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 191–202（12 aa）	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
2HBP Solution Structure of Sla1 Homology Domain 1 Deposited 2006-06-14	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 495–560（66 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K NMR sample composition 0.5mM 15N, 13C labelled SHD1, 1mM unlabeled YNENPFSDPIK peptide. PBS buffer pH 6.7, 1mM d-DTT, 1mM NaN3 \| 90% H2O, 10% D20	Resolution not provided
2JT4 Solution Structure of the Sla1 SH3-3-Ubiquitin Complex Deposited 2007-07-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 350–420（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 100% D2O \| 100% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 100% D2O \| 100% D2O	Resolution not provided
2V1Q Atomic-resolution structure of the yeast Sla1 SH3 domain 3 Deposited 2007-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 357–413（57 aa） Fragment：SH3 DOMAIN 3, RESIDUES 357-413	Not recorded	NA SODIUM ION × 1 PT PLATINUM (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å R-free 0.188
2V1Q Atomic-resolution structure of the yeast Sla1 SH3 domain 3 Deposited 2007-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 357–413（57 aa） Fragment：SH3 DOMAIN 3, RESIDUES 357-413	Not recorded	PT PLATINUM (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å R-free 0.188
3IDW Crystal structure of Sla1 homology domain 2 Deposited 2009-07-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 653–724（72 aa） Fragment：Sla1 homology domain 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；0.1 M HEPES, 5% PEG-6000, 5% MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.85 Å R-free 0.219
9HDB Sla1 SH3_3 domain (residues 355-414) Deposited 2024-11-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 355–414（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5 20% PEG 10000 1mM peptide (PVSTPARTPARTPTP) dissolved in 0.03M HEPES pH 8, 0.15M NaCl, 0.5mM TCEP	Resolution 1.49 Å R-free 0.190
9HDB Sla1 SH3_3 domain (residues 355-414) Deposited 2024-11-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 355–414（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5 20% PEG 10000 1mM peptide (PVSTPARTPARTPTP) dissolved in 0.03M HEPES pH 8, 0.15M NaCl, 0.5mM TCEP	Resolution 1.49 Å R-free 0.190

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SLA1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–60； UniProt 357–413 Author chain B； PDBConstruct 4–60； UniProt 357–413

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	1z9z
Deposition date deposition_date	2005-04-05
Structure title title	Crystal structure of yeast sla1 SH3 domain 3
Keywords keywords	SH3 DOMAIN, yeast, structural genomics, STRUCTURAL PROTEIN; STRUCTURAL 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	16.12 Å
Radius of gyration Rg (electron density) rg_electron	14.98 Å
Forward intensity I(0) i0	3786910.00
Molecular weight molecular_weight	13742.0 kDa
Excluded volume excluded_volume	17158 Å³
Envelope volume envelope_volume	19981 Å³
Hydration-shell volume shell_volume	11710 Å³
Envelope diameter envelope_diameter	55.8 Å
Shell Rg shell_rg	20.11 Å
Envelope Rg envelope_rg	15.42 Å
Shape Rg shape_rg	14.86 Å
Total Rg total_rg	16.34 Å
Total atoms total_atoms	961
Residues n_residues	120
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	56.8 Å
Rg (real space) rg_real	16.13 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	3.7870e+06
I(0) uncertainty (real space) i0_real_error	4.4290e+04
Rg (reciprocal space) rg_reciprocal	16.13 Å
I(0) (reciprocal space) i0_reciprocal	3787000.0000
Solution quality estimate total_estimate	0.8477
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.157
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1023000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.703; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.993

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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	Cytoskeleton assembly control protein SLA1
Molecular weight formula_weight	6833.8 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	1173

GMERGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPV

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1z9za1
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.34.2.0 — automated matches

Domain ID domain_id	d1z9za2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1z9zb1
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.34.2.0 — automated matches

Domain ID domain_id	d1z9zb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1z9zA00
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	1z9zB00
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	83.990 Å
Unit-cell length b length_b	83.990 Å
Unit-cell length c length_c	50.140 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1804
R_work r_work	0.1779
R_free r_free	0.2290

fit	/app/data/saxs_computation/z9/1z9z/1z9z.fit
pddf	/app/data/pr_computation/z9/1z9z/1z9z.pr.out
profile	/app/data/saxs_computation/z9/1z9z/1z9z.dat

Crystal structure of yeast sla1 SH3 domain 3

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

Cytoskeleton assembly control protein SLA1

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