SAXSdb — 1aux

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

SYNAPSIN IA

Bos taurus

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 110–420 Chain B； UniProt 110–420	Fragment：C DOMAIN	CA CALCIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.25；PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 100 MM HEPES, PH 7.25, THEN DIRECTLY TRANSFERRED TO 30 % PEG 4000, 50 MM HEPES, PH 7.5, 50 MM NACL. AFTER 12 H, CRYSTALS WERE TRANSFERRED TO 30 % PEG, 75 MM HEPES, PH 7.5, 75 MM NACL, 2.5 MM CACL2, 2.5 MM ATP-GAMMA-S FOR 23 H.	Resolution 2.30 Å R-free 0.269

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 1AUX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUV STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN Deposited 1997-09-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 110–420（311 aa） Fragment：RESIDUES 110 - 420 Chain B 110–420（311 aa） Fragment：RESIDUES 110 - 420	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.25；299 K；PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 50 MM HEPES, PH 7.25 AT 26 DEG. CELSIUS., temperature 299K	Resolution 2.15 Å R-free 0.255

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

View Construct and Data Evidence

UniProt name	SYN1_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 110–420 Author chain B； PDBConstruct 1–311； UniProt 110–420

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	1aux
Deposition date deposition_date	1997-09-06
Structure title title	STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND
Keywords keywords	SYNAPSE, PHOSPHORYLATION, SYNAPSIN IA C-DOMAIN, ATP-BINDING, TRANSFERASE; TRANSFERASE
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	30.32 Å
Radius of gyration Rg (electron density) rg_electron	29.52 Å
Forward intensity I(0) i0	72910600.00
Molecular weight molecular_weight	66962.0 kDa
Excluded volume excluded_volume	83681 Å³
Envelope volume envelope_volume	107880 Å³
Hydration-shell volume shell_volume	30279 Å³
Envelope diameter envelope_diameter	104.0 Å
Shell Rg shell_rg	36.92 Å
Envelope Rg envelope_rg	29.38 Å
Shape Rg shape_rg	29.51 Å
Total Rg total_rg	30.25 Å
Total atoms total_atoms	4698
Residues n_residues	584
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	96.4 Å
Rg (real space) rg_real	30.26 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	7.2910e+07
I(0) uncertainty (real space) i0_real_error	1.2190e+06
Rg (reciprocal space) rg_reciprocal	30.29 Å
I(0) (reciprocal space) i0_reciprocal	72910000.0000
Solution quality estimate total_estimate	0.9019
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-0.716
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24180000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.960

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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	SYNAPSIN IA
Molecular weight formula_weight	34902.0 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	4752

GAAARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSINSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLINQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATTEPFIDAKYDVRIQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMAQALPR

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
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	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1auxa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.5 — Synapsin domain

Domain ID domain_id	d1auxa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.3 — Synapsin C-terminal domain

Domain ID domain_id	d1auxb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.5 — Synapsin domain

Domain ID domain_id	d1auxb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.3 — Synapsin C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1auxA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	1auxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1auxA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	1auxB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	1auxB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1auxB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

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8. Citations (3)

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Unit-cell length a length_a	76.160 Å
Unit-cell length b length_b	76.160 Å
Unit-cell length c length_c	182.330 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2690

fit	/app/data/saxs_computation/au/1aux/1aux.fit
pddf	/app/data/pr_computation/au/1aux/1aux.pr.out
profile	/app/data/saxs_computation/au/1aux/1aux.dat

STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND

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

SYNAPSIN IA

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