SAXSdb — 6mws

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

Glutaredoxin-1

Saccharomyces cerevisiae S288c

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 2–109	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.23 M Lithium sulfate monohydrate, 0.1 M Bis-Tris, pH 5.8, 26% (w/v) PEG 3350	Resolution 1.22 Å R-free 0.172

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 6MWS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JAC Glutaredoxin Grx1p C30S mutant from yeast Deposited 2006-11-27	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 1–110（110 aa）	Mutation：YES	GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.75；50MM CITRATE PH 4.75 10-22.5% PEG 4000	Resolution 2.02 Å R-free 0.243
2JAD Yellow fluorescent protein - glutaredoxin fusion protein Deposited 2006-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 10；50MM BICARBONATE PH 10 1.5-1.75M MGSO4	Resolution 2.70 Å R-free 0.247
3C1R Crystal structure of oxidized GRX1 Deposited 2008-01-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；12% PEG 20000, 0.1M MES, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.205
3C1S Crystal structure of GRX1 in glutathionylated form Deposited 2008-01-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa）	Not recorded	GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；289 K；20% PEG 4000, 0.1M SODIUM ACETATE, 0.2M AMMONIUM DIHYDROGEN PHOSPHATE, pH 5.30, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.253

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

View Construct and Data Evidence

UniProt name	GLRX1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–114； UniProt 2–109

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	6mws
Deposition date deposition_date	2018-10-30
Structure title title	crystal structure of the reduced Grx1 from Saccharomyces cerevisiae
Keywords keywords	Glutaredoxin 1, yeast Saccharomyces cerevisiae, OXIDOREDUCTASE; OXIDOREDUCTASE
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	14.84 Å
Radius of gyration Rg (electron density) rg_electron	13.41 Å
Forward intensity I(0) i0	3024540.00
Molecular weight molecular_weight	12090.0 kDa
Excluded volume excluded_volume	15132 Å³
Envelope volume envelope_volume	16951 Å³
Hydration-shell volume shell_volume	10966 Å³
Envelope diameter envelope_diameter	47.1 Å
Shell Rg shell_rg	18.91 Å
Envelope Rg envelope_rg	13.68 Å
Shape Rg shape_rg	13.41 Å
Total Rg total_rg	14.60 Å
Total atoms total_atoms	849
Residues n_residues	108
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	47.9 Å
Rg (real space) rg_real	14.76 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.0250e+06
I(0) uncertainty (real space) i0_real_error	3.4420e+04
Rg (reciprocal space) rg_reciprocal	14.76 Å
I(0) (reciprocal space) i0_reciprocal	3025000.0000
Solution quality estimate total_estimate	0.8046
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.294
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	390600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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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	Glutaredoxin-1
Molecular weight formula_weight	12805.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	980

GPLGSMVSQETIKHVKDLIAENEIFVASKTYCPYCHAALNTLFEKLKVPRSKVLVLQLNDMKEGADIQAALYEINGQRTVPNIYINGKHIGGNDDLQELRETGELEELLEPILAN

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
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	122

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6mwsA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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8. Citations (1)

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Unit-cell length a length_a	41.364 Å
Unit-cell length b length_b	51.779 Å
Unit-cell length c length_c	57.193 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.220 Å
Low-resolution limit resolution_low	38.380 Å
R factor r_factor	0.1494
R_work r_work	0.1482
R_free r_free	0.1715

fit	/app/data/saxs_computation/mw/6mws/6mws.fit
pddf	/app/data/pr_computation/mw/6mws/6mws.pr.out
profile	/app/data/saxs_computation/mw/6mws/6mws.dat

crystal structure of the reduced Grx1 from Saccharomyces cerevisiae

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

Glutaredoxin-1

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