1bvy

COMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE CYTOCHROME P450(BM-3)

Method: X-RAY DIFFRACTION Dmax: 123.7 Å Quality: GOOD

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

PROTEIN (CYTOCHROME P450 BM-3)

Bacillus megaterium

UniProt P14779

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–458 Chain B; UniProt 1–458 Chain F; UniProt 459–649 Fragment:HEME-BINDING DOMAIN Fragment:FMN-BINDING DOMAIN HEM PROTOPORPHYRIN IX CONTAINING FE × 2 EDO 1,2-ETHANEDIOL × 5 FMN FLAVIN MONONUCLEOTIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.8;LIQUID-LIQUID FREE INTERFACE DIFFUSION AT ROOM TEMPERATURE IN PEG 8000, PIPES PH 6.8, NH4CL. Resolution 2.03 Å R-free 0.275

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.

168 other PDB entries and 311 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPXB_BACME
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–458; UniProt 1–458 Author chain B; PDBConstruct 1–458; UniProt 1–458 Author chain F; PDBConstruct 1–191; UniProt 459–649

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 1bvy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bvy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bvy
Deposition date deposition_date1998-09-21
Structure title titleCOMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE CYTOCHROME P450(BM-3)
Keywords keywordsFATTY ACID MONOOXYGENASE, HEMOPROTEIN, FLAVOPROTEIN, ELECTRON TRANSFER, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.07
Radius of gyration Rg (electron density) rg_electron35.66
Forward intensity I(0) i0213436000.00
Molecular weight molecular_weight118630.0 kDa
Excluded volume excluded_volume148580 ų
Envelope volume envelope_volume186190 ų
Hydration-shell volume shell_volume44573 ų
Envelope diameter envelope_diameter130.7
Shell Rg shell_rg40.88
Envelope Rg envelope_rg35.77
Shape Rg shape_rg35.68
Total Rg total_rg35.92
Total atoms total_atoms8361
Residues n_residues1029
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 dmax123.7
Rg (real space) rg_real36.28
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real2.1340e+08
I(0) uncertainty (real space) i0_real_error3.2220e+06
Rg (reciprocal space) rg_reciprocal36.15
I(0) (reciprocal space) i0_reciprocal213400000.0000
Solution quality estimate total_estimate0.8472
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.5
Skewness Skewness skewness0.500
Kurtosis Kurtosis kurtosis-0.336
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47150000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.884; Smooth: 0.880

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1bvya_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450
Domain ID domain_idd1bvyb_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450
Domain ID domain_idd1bvyf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.5 — Flavoproteins
Family Family familyc.23.5.1 — Flavodoxin-related

CATH v4.4 (3 domains)

Domain ID domain_id1bvyA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id1bvyB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id1bvyF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain

8. Citations (1)

9. Files and Curves (10)