SAXSdb — 4rqr

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

Glutaredoxin-1

Homo sapiens

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 2–106	Not recorded	COM 1-THIOETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；20% PEG 8K, 0.1 M phosphate citrate, 0.2M NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.08 Å R-free 0.195

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 4RQR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4Q Solution structure of human thioltransferase complex with glutathione Deposited 1998-12-25	Different construct Different mutation/modification 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 1–105（105 aa）	Mutation：C7S, C25S, C78S, C82S	GSH Glutathione × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K	Resolution not provided
1JHB HUMAN GLUTAREDOXIN IN FULLY REDUCED FORM, NMR, 20 STRUCTURES Deposited 1998-02-17	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 1–105（105 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLRX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–109； UniProt 2–106

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	4rqr
Deposition date deposition_date	2014-11-04
Structure title title	Crystal Structure of Human Glutaredoxin with MESNA
Keywords keywords	REDOX-ACTIVE CENTER, ELECTRON TRANSPORT; 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	14.96 Å
Radius of gyration Rg (electron density) rg_electron	13.38 Å
Forward intensity I(0) i0	2998820.00
Molecular weight molecular_weight	11987.0 kDa
Excluded volume excluded_volume	15041 Å³
Envelope volume envelope_volume	16976 Å³
Hydration-shell volume shell_volume	10944 Å³
Envelope diameter envelope_diameter	44.1 Å
Shell Rg shell_rg	18.93 Å
Envelope Rg envelope_rg	13.72 Å
Shape Rg shape_rg	13.35 Å
Total Rg total_rg	14.69 Å
Total atoms total_atoms	834
Residues n_residues	106
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	46.4 Å
Rg (real space) rg_real	14.87 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.9990e+06
I(0) uncertainty (real space) i0_real_error	3.4160e+04
Rg (reciprocal space) rg_reciprocal	14.88 Å
I(0) (reciprocal space) i0_reciprocal	2999000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.151
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	423800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.976

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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	11942.8 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	1077

GAGTAQEFVNCKIQPGKVVVFIKPTCPYCRRAQEILSQLPIKQGLLEFVDITATNHTNEIQDYLQQLTGARTVPRVFIGKDCIGGCSDLVSLQQSGELLTRLKQIGALQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-THIOETHANESULFONIC ACID
Molecular weight formula_weight	142.2 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	202

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4rqra1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.1 — Thioltransferase

Domain ID domain_id	d4rqra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4rqrA00
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	27.847 Å
Unit-cell length b length_b	55.414 Å
Unit-cell length c length_c	130.357 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.080 Å
Low-resolution limit resolution_low	27.710 Å
R factor r_factor	0.1734
R_work r_work	0.1722
R_free r_free	0.1952

fit	/app/data/saxs_computation/rq/4rqr/4rqr.fit
pddf	/app/data/pr_computation/rq/4rqr/4rqr.pr.out
profile	/app/data/saxs_computation/rq/4rqr/4rqr.dat

Crystal Structure of Human Glutaredoxin with MESNA

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