SAXSdb — 1rju

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

Metallothionein

OrganismNot specified

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 V； UniProt 13–48	Not recorded	CU1 COPPER (I) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；250 mM KH2PO4, 1mM LiBr, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.44 Å R-free 0.171

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 1RJU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AOO AG-SUBSTITUTED METALLOTHIONEIN FROM SACCHAROMYCES CEREVISIAE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-07-08	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–48（40 aa）	Not recorded	AG SILVER ION × 7	SOLUTION NMR NMR measurement conditions pH 6.5；283 K	Resolution not provided
1AQQ AG-SUBSTITUTED METALLOTHIONEIN FROM SACCHAROMYCES CEREVISIAE, NMR, 10 STRUCTURES Deposited 1997-07-31	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–48（40 aa）	Not recorded	AG SILVER ION × 7	SOLUTION NMR NMR measurement conditions pH 6.5；283 K	Resolution not provided
1AQR CU-METALLOTHIONEIN FROM SACCHAROMYCES CEREVISIAE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-07-31	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–48（40 aa）	Not recorded	CU1 COPPER (I) ION × 7	SOLUTION NMR NMR measurement conditions pH 6.5；283 K	Resolution not provided
1AQS CU-METALLOTHIONEIN FROM SACCHAROMYCES CEREVISIAE, NMR, 10 STRUCTURES Deposited 1997-07-31	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–61（53 aa）	Not recorded	CU1 COPPER (I) ION × 7	SOLUTION NMR NMR measurement conditions pH 6.5；283 K	Resolution not provided
1FMY HIGH RESOLUTION SOLUTION STRUCTURE OF THE PROTEIN PART OF CU7 METALLOTHIONEIN Deposited 2000-08-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–48（40 aa） Fragment：RESIDUES 9 TO 48	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 0.02；Pressure normal NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure normal NMR sample composition 5mM unenrich metallothionein; 18mM phosphate buffer; 90% H2O, 10% D2O;pH=6.5; 0.03% beta-mercaptoethanol \| 90% H2O/10% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTCU_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain V； PDBConstruct 1–36； UniProt 13–48

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	1rju
Deposition date deposition_date	2003-11-20
Structure title title	Crystal structure of a truncated form of yeast copper thionein
Keywords keywords	Yeast Cu(I) metallothionein, Cu(I) metallothionein fragments, Cu(I)-thiolate, METAL BINDING PROTEIN; METAL BINDING 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	8.84 Å
Radius of gyration Rg (electron density) rg_electron	8.26 Å
Forward intensity I(0) i0	863338.00
Molecular weight molecular_weight	4351.0 kDa
Excluded volume excluded_volume	4553 Å³
Envelope volume envelope_volume	5083 Å³
Hydration-shell volume shell_volume	5365 Å³
Envelope diameter envelope_diameter	31.7 Å
Shell Rg shell_rg	13.48 Å
Envelope Rg envelope_rg	9.15 Å
Shape Rg shape_rg	8.65 Å
Total Rg total_rg	8.96 Å
Total atoms total_atoms	265
Residues n_residues	36
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	33.6 Å
Rg (real space) rg_real	8.87 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	8.6330e+05
I(0) uncertainty (real space) i0_real_error	8.3160e+03
Rg (reciprocal space) rg_reciprocal	8.87 Å
I(0) (reciprocal space) i0_reciprocal	863300.0000
Solution quality estimate total_estimate	0.8102
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	10.2 Å
Skewness Skewness skewness	0.468
Kurtosis Kurtosis kurtosis	0.066
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.628; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.719; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1rjuv_
Class class	g — Small proteins
Fold Fold fold	g.46 — Metallothionein
Superfamily Superfamily superfamily	g.46.1 — Metallothionein
Family Family family	g.46.1.1 — Metallothionein

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8. Citations (3)

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Unit-cell length a length_a	62.167 Å
Unit-cell length b length_b	62.167 Å
Unit-cell length c length_c	62.167 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	24

Space group space_group	P 43 3 2
Space-group number int_tables_number	212
Crystal system crystal_system	—

Resolution resolution	1.440 Å
Low-resolution limit resolution_low	27.840 Å
R factor r_factor	0.1469
R_work r_work	0.1448
R_free r_free	0.1707

Description description	Metallothionein
Molecular weight formula_weight	3847.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	V
Atom count atom_count	302

Crystal structure of a truncated form of yeast copper thionein

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

Metallothionein

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	8

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

fit	/app/data/saxs_computation/rj/1rju/1rju.fit
pddf	/app/data/pr_computation/rj/1rju/1rju.pr.out
profile	/app/data/saxs_computation/rj/1rju/1rju.dat