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- PDB-9yvv: Cocrystallized structure of Bmp7 in complex with 2,4-dibromophenol -

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Basic information

Entry
Database: PDB / ID: 9yvv
TitleCocrystallized structure of Bmp7 in complex with 2,4-dibromophenol
ComponentsPolybrominated aromatic compounds synthase
KeywordsOXIDOREDUCTASE / cytochrome P450 enzyme / biaryl coupling
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water / steroid 17-alpha-monooxygenase activity / hormone biosynthetic process / progesterone metabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 2,4-bis(bromanyl)phenol / Polybrominated aromatic compounds synthase
Similarity search - Component
Biological speciesMarinomonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsNolan, K. / Wang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128742 United States
CitationJournal: Acs Catalysis / Year: 2025
Title: Bacterial Cytochrome P450 for Oxidative Halogenated Biaryl Coupling
Authors: Petriti, V. / Nolan, K. / Xu, W. / Tsai, S. / Wang, X. / Xie, W.J. / Zheng, G. / Wang, Y. / Ding, Y.
History
DepositionOct 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polybrominated aromatic compounds synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9188
Polymers56,4861
Non-polymers1,4327
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.220, 101.220, 159.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polybrominated aromatic compounds synthase / CYP450 Bmp7


Mass: 56486.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (bacteria) / Gene: bmp7, Marme_4095 / Production host: Escherichia coli (E. coli)
References: UniProt: F2K081, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water

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Non-polymers , 5 types, 227 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-Y8I / 2,4-bis(bromanyl)phenol


Mass: 251.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4Br2O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.62 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350 and 0.2 M of sodium citrate tribasic dihydrate. Enzyme was premixed with 2.5 eq substrate before wells were set.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 40817 / % possible obs: 97.4 % / Redundancy: 4.6 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.07 / Rrim(I) all: 0.155 / Χ2: 0.645 / Net I/σ(I): 5 / Num. measured all: 187795
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.32-2.363.10.78216610.8470.9580.4490.9070.49179.9
2.36-2.43.20.87818190.8140.9470.4971.0150.46787.6
2.4-2.453.40.89419150.8090.9460.51.030.47595
2.45-2.53.80.78520500.8550.960.4290.8990.47598.4
2.5-2.554.20.84320250.8660.9630.4490.9590.47298.2
2.55-2.614.60.75620600.90.9730.3850.8510.47299.5
2.61-2.684.90.68120570.9350.9830.3380.7620.48399.9
2.68-2.7550.63320820.9220.980.3120.7080.482100
2.75-2.835.10.49920840.9540.9880.2420.5560.494100
2.83-2.9250.43220640.9670.9920.2120.4830.51799.9
2.92-3.0350.34520670.9680.9920.170.3860.524100
3.03-3.154.90.25121000.9810.9950.1240.2810.568100
3.15-3.294.90.2120760.9830.9960.1050.2360.573100
3.29-3.474.80.16120700.9890.9970.0810.180.63299.7
3.47-3.684.80.11720700.9930.9980.0590.1310.67998.5
3.68-3.974.70.08120970.9950.9990.0420.0920.77999.4
3.97-4.3750.0721080.9940.9990.0350.0780.86599.7
4.37-550.06321200.9960.9990.0310.070.93499.3
5-6.294.90.06321340.9970.9990.0310.0710.92998.7
6.29-504.80.0521580.9970.9990.0250.0561.22495.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→45.55 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1989 4.92 %
Rwork0.1927 --
obs0.1946 40455 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 80 220 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073984
X-RAY DIFFRACTIONf_angle_d0.8485399
X-RAY DIFFRACTIONf_dihedral_angle_d8.629523
X-RAY DIFFRACTIONf_chiral_restr0.048563
X-RAY DIFFRACTIONf_plane_restr0.009698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.3581100.31852217X-RAY DIFFRACTION79
2.38-2.440.3581320.31152569X-RAY DIFFRACTION91
2.44-2.510.33271390.29912697X-RAY DIFFRACTION97
2.51-2.590.30311420.2752742X-RAY DIFFRACTION97
2.59-2.680.27631410.24772740X-RAY DIFFRACTION98
2.68-2.790.29841490.23932795X-RAY DIFFRACTION99
2.79-2.920.27371430.22252788X-RAY DIFFRACTION99
2.92-3.070.25041470.22922810X-RAY DIFFRACTION99
3.07-3.270.27331490.21032827X-RAY DIFFRACTION100
3.27-3.520.2651430.19562800X-RAY DIFFRACTION99
3.52-3.870.20161430.16492822X-RAY DIFFRACTION99
3.87-4.430.17851500.14172865X-RAY DIFFRACTION100
4.43-5.580.16581520.14832886X-RAY DIFFRACTION99
5.59-45.550.20481490.16812908X-RAY DIFFRACTION96

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