SAXSdb — 4rg3

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

Cyclohexanone monooxygenase

Rhodococcus sp. HI-31

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 1–540	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 ECE Caprolactone × 1 BCN BICINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；60% PEG 3350, 0.1 M bicine, 0.1 M epsilon-caprolactone, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.94 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 4RG3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UCL Cyclohexanone-bound crystal structure of cyclohexanone monooxygenase in the Rotated conformation Deposited 2011-10-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 CYH CYCLOHEXANONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1 M imidazole, 0.2% TMOS, 20% PEG 3350, 0.1 M cyclohexanone, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.36 Å R-free 0.264
4RG4 Epsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Loose conformation Deposited 2014-09-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 ECE Caprolactone × 1 PTD PENTANEDIAL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；40% PEG 3350, 0.1 M imidazole, 0.2 M epsilon-caprolactone; crystals were transferred to a fresh drop and cross-linked with glutaraldehyde, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.51 Å R-free 0.264

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

View Construct and Data Evidence

UniProt name	C0STX7_9NOCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–548； UniProt 1–540

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	4rg3
Deposition date deposition_date	2014-09-29
Structure title title	Epsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Tight conformation
Keywords keywords	;Baeyer-Villiger monooxygenase, Baeyer-Villiger oxidation, biocatalysis, flavoprotein, green chemistry, protein engineering, Rossmann fold, Oxidoreductase, FAD, NADPH, cyclohexanone, oxygen, Cytosolic (bacterial) ;; 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	24.31 Å
Radius of gyration Rg (electron density) rg_electron	23.19 Å
Forward intensity I(0) i0	58122400.00
Molecular weight molecular_weight	59041.0 kDa
Excluded volume excluded_volume	73597 Å³
Envelope volume envelope_volume	83862 Å³
Hydration-shell volume shell_volume	29505 Å³
Envelope diameter envelope_diameter	76.7 Å
Shell Rg shell_rg	31.06 Å
Envelope Rg envelope_rg	23.38 Å
Shape Rg shape_rg	23.18 Å
Total Rg total_rg	24.10 Å
Total atoms total_atoms	4180
Residues n_residues	529
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	75.4 Å
Rg (real space) rg_real	24.18 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	5.8120e+07
I(0) uncertainty (real space) i0_real_error	7.5530e+05
Rg (reciprocal space) rg_reciprocal	24.21 Å
I(0) (reciprocal space) i0_reciprocal	58120000.0000
Solution quality estimate total_estimate	0.9033
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.225
Kurtosis Kurtosis kurtosis	-0.424
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13060000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cyclohexanone monooxygenase
Molecular weight formula_weight	60808.6 kDa
EC 编号 ec_number	1.14.13.22
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	4323

GSLEASMHMTAQTTHTVDAVVIGAGFGGIYAVHKLHHELGLTTVGFDKADGPGGTWYWNRYPGALSDTESHLYRFSFDRDLLQESTWKTTYITQPEILEYLEDVVDRFDLRRHFKFGTEVTSALYLDDENLWEVTTDHGEVYRAKYVVNAVGLLSAINFPNLPGLDTFEGETIHTAAWPEGKSLAGRRVGVIGTGSTGQQVITSLAPEVEHLTVFVRTPQYSVPVGNRPVNPEQIAEIKADYDRIWERAKNSAVAFGFEESTLPAMSVSEEERNRIFQEAWDHGGGFRFMFGTFGDIATDEAANEAAASFIRAKVAEIIEDPETARKLMPKGLFAKRPLCDSGYYEVYNRPNVEAVAIKENPIREVTAKGVVTEDGVLHELDVLVFATGFDAVDGNYRRIEIRGRDGLHINDHWDGQPTSYLGVSTANFPNWFMVLGPNGPFTNLPPSIETQVEWISDTIGYAERNGVRAIEPTPEAEAEWTETCTEIANATLFTKGDSWIFGANIPGKKPSVLFYLGGLRNYRAVMAEVAADGYRGFEVKSAEMVTV

来源 Source

来源生物 organism	Rhodococcus sp. HI-31
NCBI Class编号 ncbi_taxonomy_id	638919
宿主生物 host_organism	Escherichia coli

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	1

Entity 3 Entity 3 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	Caprolactone
Molecular weight formula_weight	114.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BICINE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4rg3A01
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

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8. Citations (1)

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Unit-cell length a length_a	55.698 Å
Unit-cell length b length_b	67.060 Å
Unit-cell length c length_c	131.641 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	1.940 Å
Low-resolution limit resolution_low	24.030 Å
R factor r_factor	0.1700
R_work r_work	0.1646
R_free r_free	0.2179

fit	/app/data/saxs_computation/rg/4rg3/4rg3.fit
pddf	/app/data/pr_computation/rg/4rg3/4rg3.pr.out
profile	/app/data/saxs_computation/rg/4rg3/4rg3.dat

Epsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Tight conformation

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

Cyclohexanone monooxygenase

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