SAXSdb — 1q1r

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

Putidaredoxin reductase

Pseudomonas putida

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 1–422	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；lithium sulfate, lithium acetate, lithium formate, bis-tris propane, glycerol, dithiothreitol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.91 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–422	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；lithium sulfate, lithium acetate, lithium formate, bis-tris propane, glycerol, dithiothreitol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.91 Å R-free 0.236

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 1Q1R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Q1W Crystal Structure of Putidaredoxin Reductase from Pseudomonas putida Deposited 2003-07-22	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–422（422 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；lithium sulfate, lithium acetate, lithium formate, bis-tris propane, glycerol, dithiothreitol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.240
1Q1W Crystal Structure of Putidaredoxin Reductase from Pseudomonas putida Deposited 2003-07-22	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–422（422 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；lithium sulfate, lithium acetate, lithium formate, bis-tris propane, glycerol, dithiothreitol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.240
3LB8 Crystal structure of the covalent putidaredoxin reductase-putidaredoxin complex Deposited 2010-01-07	Different construct 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 2–422（421 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；1.3 M malonate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.272
3LB8 Crystal structure of the covalent putidaredoxin reductase-putidaredoxin complex Deposited 2010-01-07	Different construct 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 2–422（421 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；1.3 M malonate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.272

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

View Construct and Data Evidence

UniProt name	CAMA_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–422； UniProt 1–422 Author chain B； PDBConstruct 1–422； UniProt 1–422

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	1q1r
Deposition date deposition_date	2003-07-22
Structure title title	Crystal Structure of Putidaredoxin Reductase from Pseudomonas putida
Keywords keywords	glutathione reductase fold, 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	32.25 Å
Radius of gyration Rg (electron density) rg_electron	31.51 Å
Forward intensity I(0) i0	138316000.00
Molecular weight molecular_weight	92415.0 kDa
Excluded volume excluded_volume	115320 Å³
Envelope volume envelope_volume	145090 Å³
Hydration-shell volume shell_volume	38828 Å³
Envelope diameter envelope_diameter	114.1 Å
Shell Rg shell_rg	38.20 Å
Envelope Rg envelope_rg	31.48 Å
Shape Rg shape_rg	31.52 Å
Total Rg total_rg	32.01 Å
Total atoms total_atoms	6500
Residues n_residues	842
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	104.8 Å
Rg (real space) rg_real	32.26 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.3830e+08
I(0) uncertainty (real space) i0_real_error	2.3220e+06
Rg (reciprocal space) rg_reciprocal	32.26 Å
I(0) (reciprocal space) i0_reciprocal	138300000.0000
Solution quality estimate total_estimate	0.8935
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.331
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50140000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.900

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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	Putidaredoxin reductase
Molecular weight formula_weight	46780.2 kDa
EC 编号 ec_number	1.18.1.-
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	7158

MNANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATVIPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVILSDGRALDYDRLVLATGGRPRPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIGLIPNCELASAAGLQVDNGIVINEHMQTSDPLIMAVGDCARFHSQLYDRWVRIESVPNALEQARKIAAILCGKVPRDEAAPWFWSDQYEIGLKMVGLSEGYDRIIVRGSLAQPDFSVFYLQGDRVLAVDTVNRPVEFNQSKQIITDRLPVEPNLLGDESVPLKEIIAAAKAELSSAPARHHHHHH

来源 Source

来源生物 organism	Pseudomonas putida
NCBI Class编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 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	658

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1q1ra1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1q1ra2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1q1ra3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

Domain ID domain_id	d1q1rb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1q1rb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1q1rb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

CATH v4.4 (6 domains)

Domain ID domain_id	1q1rA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1q1rA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1q1rA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	1q1rB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1q1rB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1q1rB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

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8. Citations (1)

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Unit-cell length a length_a	70.780 Å
Unit-cell length b length_b	104.130 Å
Unit-cell length c length_c	166.780 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.910 Å
Low-resolution limit resolution_low	29.570 Å
R factor r_factor	—
R_work r_work	0.2126
R_free r_free	0.2358

fit	/app/data/saxs_computation/q1/1q1r/1q1r.fit
pddf	/app/data/pr_computation/q1/1q1r/1q1r.pr.out
profile	/app/data/saxs_computation/q1/1q1r/1q1r.dat

Crystal Structure of Putidaredoxin Reductase from Pseudomonas putida

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

Putidaredoxin 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