3b3r

Crystal structure of Streptomyces cholesterol oxidase H447Q/E361Q mutant bound to glycerol (0.98A)

Method: X-RAY DIFFRACTION Dmax: 77.3 Å Quality: REASONABLE

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

Cholesterol oxidase

Streptomyces sp.

UniProt P12676

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 42–546 Mutation:E361Q/H447Q SO4 SULFATE ION × 2 FAE FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.2;291 K;10% PEG 8000, 75mM magnesium sulfate, 100mM cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 0.98 Å R-free 0.159

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.

22 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHOD_STRS0
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–506; UniProt 42–546

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3b3r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3b3r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3b3r
Deposition date deposition_date2007-10-22
Structure title titleCrystal structure of Streptomyces cholesterol oxidase H447Q/E361Q mutant bound to glycerol (0.98A)
Keywords keywords;flavoenzyme, flavin, cholesterol oxidase, covalently-modified flavin, Cholesterol metabolism, FAD, Flavoprotein, Lipid metabolism, Oxidoreductase, Secreted, Steroid metabolism ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.08
Radius of gyration Rg (electron density) rg_electron21.95
Forward intensity I(0) i053090100.00
Molecular weight molecular_weight55678.0 kDa
Excluded volume excluded_volume69106 ų
Envelope volume envelope_volume77568 ų
Hydration-shell volume shell_volume28484 ų
Envelope diameter envelope_diameter79.5
Shell Rg shell_rg29.80
Envelope Rg envelope_rg22.17
Shape Rg shape_rg21.94
Total Rg total_rg22.79
Total atoms total_atoms7263
Residues n_residues503
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.3
Rg (real space) rg_real22.96
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real5.3090e+07
I(0) uncertainty (real space) i0_real_error7.1350e+05
Rg (reciprocal space) rg_reciprocal22.99
I(0) (reciprocal space) i0_reciprocal53090000.0000
Solution quality estimate total_estimate0.6802
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.296
Angular range angular_range— – 0.3450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14050000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 0.171; Positv: 1.000; Valcen: 0.999; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3b3ra1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.2 — FAD-linked reductases, N-terminal domain
Domain ID domain_idd3b3ra2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.1 — GMC oxidoreductases
Domain ID domain_idd3b3ra3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id3b3rA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id3b3rA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology410 — Cholesterol Oxidase; domain 2
Homologous superfamily homologous superfamily10 — Cholesterol Oxidase; domain 2

8. Citations (1)

9. Files and Curves (10)