SAXSdb — 2jtt

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

Protein S100-A6

Oryctolagus cuniculus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–90 Chain B； UniProt 1–90	Not recorded	Calcyclin-binding protein × 2 （Q9CXW3）	SOLUTION NMR NMR measurement conditions：pH 6.5；318 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE \| 93% H2O/5% D2O/2% d-TFE NMR sample composition：1 mM [U-100% 15N] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE \| 93% H2O/5% D2O/2% d-TFE NMR sample composition：1 mM [U-100% 13C] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 98% D2O/2% d-TFE \| 98% D2O/2% d-TFE NMR sample composition：2.3 mM [U-100% 13C] SIP(189-219), 2.3 mM [U-100% 15N] S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE \| 93% H2O/5% D2O/2% d-TFE	Resolution not provided

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 2JTT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A03 THE THREE-DIMENSIONAL STRUCTURE OF CA2+-BOUND CALCYCLIN: IMPLICATIONS FOR CA2+-SIGNAL TRANSDUCTION BY S100 PROTEINS, NMR, 20 STRUCTURES Deposited 1997-12-08	Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa） Chain B 1–90（90 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 50mM TRIS, 20-38mM CACL2 NMR sample composition 95% H2O, 5% D2O	Resolution not provided
1CNP THE STRUCTURE OF CALCYCLIN REVEALS A NOVEL HOMODIMERIC FOLD FOR S100 CA2+-BINDING PROTEINS, NMR, 22 STRUCTURES Deposited 1995-08-31	Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa） Chain B 1–90（90 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1JWD Ca2+-induced Structural Changes in Calcyclin: High-resolution Solution Structure of Ca2+-bound Calcyclin. Deposited 2001-09-04	Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa） Chain B 1–90（90 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 30 mM CaCl2；Pressure ambient NMR sample composition 2 mM calcyclin, 50 MM TRIS buffer, 30 mM CaCl2 \| 90% H2O/10% D2O NMR sample composition 2 mM 15N, 13C-enriched calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl2 \| 90% H2O/10% D2O NMR sample composition 1:1 15N,13C-enriched:unlabled calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl2 \| 90% H2O/10% D2O NMR sample composition 15N-enriched calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl2 \| 90% H2O/10% D2O NMR sample composition 10% 13C-enriched calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl2 \| D2O	Resolution not provided
2CNP HIGH RESOLUTION SOLUTION STRUCTURE OF APO RABBIT CALCYCLIN, NMR, 22 STRUCTURES Deposited 1999-01-07	Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa） Chain B 1–90（90 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K	Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S10A6_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–90； UniProt 1–90 Author chain B； PDBConstruct 1–90； UniProt 1–90

Calcyclin-binding protein

Mus musculus

UniProt Q9CXW3

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 189–219 Chain D； UniProt 189–219	Fragment：S100A6 binding domain	Protein S100-A6 × 2 （P30801）	SOLUTION NMR NMR measurement conditions：pH 6.5；318 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE \| 93% H2O/5% D2O/2% d-TFE NMR sample composition：1 mM [U-100% 15N] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE \| 93% H2O/5% D2O/2% d-TFE NMR sample composition：1 mM [U-100% 13C] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 98% D2O/2% d-TFE \| 98% D2O/2% d-TFE NMR sample composition：2.3 mM [U-100% 13C] SIP(189-219), 2.3 mM [U-100% 15N] S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE \| 93% H2O/5% D2O/2% d-TFE	Resolution not provided

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 2JTT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YSM NMR Structure of N-terminal domain (Residues 1-77) of Siah-Interacting Protein. Deposited 2005-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–77（77 aa） Fragment：N-Terminal Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 20 mM NaPi, 50 mM NaCl；Pressure 1 NMR sample composition 1 mM 15N/13C-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl \| 90% H2O/10% D2O NMR sample composition 1 mM 15N-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl \| 90% H2O/10% D2O NMR sample composition 1 mM U-SIP(1-77), 20 mM NaPi, 50 mM NaCl \| 90% H2O/10% D2O NMR sample composition 1 mM 13C-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl \| 100% D2O NMR sample composition 1 mM 10% 13C-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl \| 100% D2O NMR sample composition 1 mM U-SIP(1-77), 20 mM NaPi, 50 mM NaCl \| 100% 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	CYBP_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–35； UniProt 189–219 Author chain D； PDBConstruct 5–35； UniProt 189–219

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	2jtt
Deposition date deposition_date	2007-08-06
Structure title title	Solution structure of calcium loaded S100A6 bound to C-terminal Siah-1 interacting protein
Keywords keywords	;S100A6, Siah-1 interacting protein, ubiquitination, E3 ligase complex, beta-catenin, Calcium, Cell cycle, Mitogen, Cytoplasm, Nucleus, Phosphorylation, Ubl conjugation pathway, calcium binding protein-antitumor protein COMPLEX ;; calcium binding protein/antitumor protein
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.46 Å
Radius of gyration Rg (electron density) rg_electron	17.84 Å
Forward intensity I(0) i0	4039420000.00
Molecular weight molecular_weight	551670.0 kDa
Excluded volume excluded_volume	695260 Å³
Envelope volume envelope_volume	63338 Å³
Hydration-shell volume shell_volume	25337 Å³
Envelope diameter envelope_diameter	66.2 Å
Shell Rg shell_rg	27.57 Å
Envelope Rg envelope_rg	20.17 Å
Shape Rg shape_rg	17.80 Å
Total Rg total_rg	18.09 Å
Total atoms total_atoms	78120
Residues n_residues	4840
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	55.4 Å
Rg (real space) rg_real	18.31 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	4.0390e+09
I(0) uncertainty (real space) i0_real_error	4.8040e+07
Rg (reciprocal space) rg_reciprocal	18.34 Å
I(0) (reciprocal space) i0_reciprocal	4039000000.0000
Solution quality estimate total_estimate	0.8235
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.016
Kurtosis Kurtosis kurtosis	-0.507
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1265000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein S100-A6
Molecular weight formula_weight	10167.7 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	78120

MASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG

来源 Source

来源生物 organism	Oryctolagus cuniculus
通用名 common_name	rabbit
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calcyclin-binding protein
Molecular weight formula_weight	3946.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GPGSSEGLMNVLKKIYEDGDDDMKRTINKAWVESR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2jtta_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

Domain ID domain_id	d2jttb_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

CATH v4.4 (2 domains)

Domain ID domain_id	2jttA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2jttB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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fit	/app/data/saxs_computation/jt/2jtt/2jtt.fit
pddf	/app/data/pr_computation/jt/2jtt/2jtt.pr.out
profile	/app/data/saxs_computation/jt/2jtt/2jtt.dat

Solution structure of calcium loaded S100A6 bound to C-terminal Siah-1 interacting protein

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

Protein S100-A6

State in the Current Structure

Other States of the Same Protein in the Database

Calcyclin-binding protein

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)