SAXSdb — 1gy1

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

RUSTICYANIN

THIOBACILLUS FERROOXIDANS

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 33–187	Mutation：YES	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；pH 5.00	Resolution 1.65 Å R-free 0.190
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 33–187	Mutation：YES	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；pH 5.00	Resolution 1.65 Å R-free 0.190

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 1GY1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3Z REDUCED RUSTICYANIN AT 1.9 ANGSTROMS Deposited 1998-01-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–187（155 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；VAPOR DIFFUSION IN HANGING DROPS AGAINST 100 MM-SODIUM CITRATE, PH 4.6, 200 MM LITHIUM CHLORIDE AND 25%(W/V) PEG 8000 AT 277K. CRYSTALS SOAKED IN 10MM DITHIONITE FOR 3 DAYS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.272
1A8Z STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN AT 2.1A RESOLUTION USING ANOMALOUS SCATTERING DATA WITH DIRECT METHODS Deposited 1998-03-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–187（153 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.8；SIMILAR TO THOSE DESCRIBED IN DJEBLI ET AL., J. MOL. BIOL. 229, 581 (1992)., pH 3.8	Resolution 2.10 Å R-free 0.219
1CUR REDUCED RUSTICYANIN, NMR Deposited 1996-04-19	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa）	Not recorded	CU COPPER (II) ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1RCY RUSTICYANIN (RC) FROM THIOBACILLUS FERROOXIDANS Deposited 1996-04-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–187（150 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.90 Å R-free 0.252
2CAK 1.27Angstrom Structure of Rusticyanin from Thiobacillus ferrooxidans Deposited 2005-12-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–187（153 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.8；pH 3.80	Resolution 1.27 Å R-free 0.138
2CAL Crystal structure of His143Met rusticyanin Deposited 2005-12-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–187（153 aa）	Mutation：YES	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.10 Å R-free 0.170

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

View Construct and Data Evidence

UniProt name	RUS2_THIFE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–155； UniProt 33–187 Author chain B； PDBConstruct 1–155； UniProt 33–187

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	1gy1
Deposition date deposition_date	2002-04-16
Structure title title	Crystal structures of Ser86Asp and Met148Leu Rusticyanin
Keywords keywords	S86D, M148L, RUSTICYANIN, MUTANT, METAL-BINDING, ELECTRON TRANSPORT, PERIPLASMIC; ELECTRON TRANSPORT
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	22.17 Å
Radius of gyration Rg (electron density) rg_electron	21.64 Å
Forward intensity I(0) i0	17151800.00
Molecular weight molecular_weight	33082.0 kDa
Excluded volume excluded_volume	42032 Å³
Envelope volume envelope_volume	47768 Å³
Hydration-shell volume shell_volume	19216 Å³
Envelope diameter envelope_diameter	76.5 Å
Shell Rg shell_rg	27.30 Å
Envelope Rg envelope_rg	21.84 Å
Shape Rg shape_rg	21.60 Å
Total Rg total_rg	22.53 Å
Total atoms total_atoms	2334
Residues n_residues	308
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	77.1 Å
Rg (real space) rg_real	22.27 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.7150e+07
I(0) uncertainty (real space) i0_real_error	2.2290e+05
Rg (reciprocal space) rg_reciprocal	22.25 Å
I(0) (reciprocal space) i0_reciprocal	17150000.0000
Solution quality estimate total_estimate	0.8448
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.423
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4206000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.785; Smooth: 0.973

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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	RUSTICYANIN
Molecular weight formula_weight	16595.0 kDa
Mutation mutation	YES
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	2555

GTLDTTWKEATLPQVKAMLQKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLQIPAGATVDVTFINTNKGFGHDFDITKKGPPYAVMPVIDPIVAGTGFSPVPKDGKFGYTNFTWHPTAGTYYYVCQIPGHAATGMFGKIVVK

来源 Source

来源生物 organism	THIOBACILLUS FERROOXIDANS
NCBI Class编号 ncbi_taxonomy_id	920
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	217

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1gy1a_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d1gy1b_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1gy1A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1gy1B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (1)

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Unit-cell length a length_a	43.098 Å
Unit-cell length b length_b	61.408 Å
Unit-cell length c length_c	53.346 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	52.700 Å
R factor r_factor	0.1670
R_work r_work	0.1660
R_free r_free	0.1900

fit	/app/data/saxs_computation/gy/1gy1/1gy1.fit
pddf	/app/data/pr_computation/gy/1gy1/1gy1.pr.out
profile	/app/data/saxs_computation/gy/1gy1/1gy1.dat

Crystal structures of Ser86Asp and Met148Leu Rusticyanin

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

RUSTICYANIN

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