SAXSdb — 1ff3

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

PEPTIDE METHIONINE SULFOXIDE REDUCTASE

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 A； UniProt 1–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218
4	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–211 Chain B； UniProt 1–211 Chain C； UniProt 1–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218
5	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–211 Chain B； UniProt 1–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–211 Chain C； UniProt 1–211	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218

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 1FF3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GT3 Solution structure and dynamics of the reduced form of Methionine Sulfoxide Reductase A from Escherichia coli, a 23 kDa protein Deposited 2006-04-27	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 1–211（211 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.1；298 K；Pressure 1 NMR sample composition 1 mM MsrA, 1mM DTT, 50 mM KPi, pH 7.1, 90 % H2O, 10 % D2O \| 90% H2O/10% D2O	Resolution not provided
2IEM Solution structure of an oxidized form (Cys51-Cys198) of E. coli Methionine Sulfoxide Reductase A (MsrA) Deposited 2006-09-19	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 1–211（211 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.1；298 K NMR sample composition 1 mM MsrA U-15N,13C; 50 mM phosphate buffer NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
6YEV Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli Deposited 2020-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa）	Mutation：Cys51Ala, Cys86Ala, Cys198Ala	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.1M BIS-TRIS propane pH 6.5, 0.2M trisodium citrate, 20% PEG 3350	Resolution 2.94 Å R-free 0.258
6YEV Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli Deposited 2020-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–212（212 aa）	Mutation：Cys51Ala, Cys86Ala, Cys198Ala	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.1M BIS-TRIS propane pH 6.5, 0.2M trisodium citrate, 20% PEG 3350	Resolution 2.94 Å R-free 0.258
6YEV Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli Deposited 2020-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–212（212 aa）	Mutation：Cys51Ala, Cys86Ala, Cys198Ala	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.1M BIS-TRIS propane pH 6.5, 0.2M trisodium citrate, 20% PEG 3350	Resolution 2.94 Å R-free 0.258
6YEV Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli Deposited 2020-03-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–212（212 aa）	Mutation：Cys51Ala, Cys86Ala, Cys198Ala	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.1M BIS-TRIS propane pH 6.5, 0.2M trisodium citrate, 20% PEG 3350	Resolution 2.94 Å R-free 0.258

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

View Construct and Data Evidence

UniProt name	MSRA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 1–211 Author chain B； PDBConstruct 1–211； UniProt 1–211 Author chain C； PDBConstruct 1–211； UniProt 1–211

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	1ff3
Deposition date deposition_date	2000-07-25
Structure title title	STRUCTURE OF THE PEPTIDE METHIONINE SULFOXIDE REDUCTASE FROM ESCHERICHIA COLI
Keywords keywords	peptide methionine sulfoxide reductase, alpha beta roll, pmsr, msra, 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	29.31 Å
Radius of gyration Rg (electron density) rg_electron	28.65 Å
Forward intensity I(0) i0	76521900.00
Molecular weight molecular_weight	65813.0 kDa
Excluded volume excluded_volume	80746 Å³
Envelope volume envelope_volume	102350 Å³
Hydration-shell volume shell_volume	29914 Å³
Envelope diameter envelope_diameter	93.1 Å
Shell Rg shell_rg	35.75 Å
Envelope Rg envelope_rg	28.13 Å
Shape Rg shape_rg	28.64 Å
Total Rg total_rg	29.31 Å
Total atoms total_atoms	4623
Residues n_residues	587
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	91.6 Å
Rg (real space) rg_real	29.25 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	7.6520e+07
I(0) uncertainty (real space) i0_real_error	9.9800e+05
Rg (reciprocal space) rg_reciprocal	29.28 Å
I(0) (reciprocal space) i0_reciprocal	76520000.0000
Solution quality estimate total_estimate	0.9105
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.5 Å
Skewness Skewness skewness	0.169
Kurtosis Kurtosis kurtosis	-0.698
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9566000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.963

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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) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ff3a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.1 — Peptide methionine sulfoxide reductase

Domain ID domain_id	d1ff3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.1 — Peptide methionine sulfoxide reductase

Domain ID domain_id	d1ff3c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.1 — Peptide methionine sulfoxide reductase

CATH v4.4 (3 domains)

Domain ID domain_id	1ff3A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

Domain ID domain_id	1ff3B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

Domain ID domain_id	1ff3C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

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8. Citations (1)

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Unit-cell length a length_a	102.500 Å
Unit-cell length b length_b	102.500 Å
Unit-cell length c length_c	292.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1950
R_free r_free	0.2180

Description description	PEPTIDE METHIONINE SULFOXIDE REDUCTASE
Molecular weight formula_weight	23308.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5153

STRUCTURE OF THE PEPTIDE METHIONINE SULFOXIDE REDUCTASE FROM ESCHERICHIA COLI

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

PEPTIDE METHIONINE SULFOXIDE REDUCTASE

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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	530

fit	/app/data/saxs_computation/ff/1ff3/1ff3.fit
pddf	/app/data/pr_computation/ff/1ff3/1ff3.pr.out
profile	/app/data/saxs_computation/ff/1ff3/1ff3.dat