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9ms3

Crystal structure of Bmp7 in complex with 2,4-dibromophenol generated by substrate soaking

Method: X-RAY DIFFRACTION Dmax: 71.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polybrominated aromatic compounds synthase

Marinomonas mediterranea

UniProt F2K081

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 1–495 Not recorded GOL GLYCEROL × 5 CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 Y8I 2,4-bis(bromanyl)phenol × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；278 K；20% PEG 3350 and 0.2 M of sodium citrate tribasic dihydrate Resolution 2.25 Å R-free 0.229

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 9MS3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YV5 Crystal structure of cytochrome P450 enzyme Bmp7 Deposited 2025-10-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；20% PEG 3350 and 0.2 M of sodium citrate tribasic dihydrate
Resolution 2.28 Å R-free 0.248
9YVV Cocrystallized structure of Bmp7 in complex with 2,4-dibromophenol Deposited 2025-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Not recorded GOL GLYCEROL × 3 CL CHLORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 Y8I 2,4-bis(bromanyl)phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；20% PEG 3350 and 0.2 M of sodium citrate tribasic dihydrate. Enzyme was premixed with 2.5 eq substrate before wells were set.
Resolution 2.32 Å R-free 0.230

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

View Construct and Data Evidence
UniProt name BMP7_MARM1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–495； UniProt 1–495

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 9ms3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ms3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ms3
Deposition date deposition_date2025-01-09
Structure title titleCrystal structure of Bmp7 in complex with 2,4-dibromophenol generated by substrate soaking
Keywords keywordscytochrome P450 enzyme, biaryl coupling, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.71 Å
Radius of gyration Rg (electron density) rg_electron22.44 Å
Forward intensity I(0) i051372800.00
Molecular weight molecular_weight55695.0 kDa
Excluded volume excluded_volume69438 ų
Envelope volume envelope_volume79320 ų
Hydration-shell volume shell_volume28581 ų
Envelope diameter envelope_diameter74.4 Å
Shell Rg shell_rg30.31 Å
Envelope Rg envelope_rg22.73 Å
Shape Rg shape_rg22.47 Å
Total Rg total_rg23.21 Å
Total atoms total_atoms3910
Residues n_residues475
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.7 Å
Rg (real space) rg_real23.56 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real5.1370e+07
I(0) uncertainty (real space) i0_real_error6.9250e+05
Rg (reciprocal space) rg_reciprocal23.60 Å
I(0) (reciprocal space) i0_reciprocal51370000.0000
Solution quality estimate total_estimate0.8321
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1 Å
Skewness Skewness skewness0.137
Kurtosis Kurtosis kurtosis-0.524
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10330000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)