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- PDB-9ms3: Crystal structure of Bmp7 in complex with 2,4-dibromophenol gener... -

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Basic information

Entry
Database: PDB / ID: 9ms3
TitleCrystal structure of Bmp7 in complex with 2,4-dibromophenol generated by substrate soaking
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: 2.25 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
DepositionJan 9, 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)58,13811
Polymers56,4861
Non-polymers1,65210
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-40 kcal/mol
Surface area19300 Å2
Unit cell
Length a, b, c (Å)102.096, 102.096, 159.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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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 BL21(DE3) (bacteria)
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, 277 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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.: 267 / 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: 4.26 Å3/Da / Density % sol: 71.13 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350 and 0.2 M of sodium citrate tribasic dihydrate

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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: 2.25→50 Å / Num. obs: 42958 / % possible obs: 97.7 % / Redundancy: 11.3 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.046 / Rrim(I) all: 0.159 / Χ2: 0.749 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.296.90.82418530.8970.9720.2780.8740.50781.1
2.29-2.337.50.76918900.9240.980.2570.8140.50983.3
2.33-2.387.70.91821040.8970.9720.3080.9730.50591.1
2.38-2.428.20.94322120.8850.9690.3180.9990.49597.8
2.42-2.489.30.87822630.9190.9790.290.9260.599.9
2.48-2.5310.60.81623200.9520.9880.2580.8570.505100
2.53-2.611.70.72222770.9750.9940.2180.7550.506100
2.6-2.6712.50.61922820.9780.9950.1810.6460.514100
2.67-2.7512.70.58423020.9720.9930.170.6090.531100
2.75-2.8312.80.45622770.9830.9960.1310.4750.553100
2.83-2.9412.70.40322890.990.9970.1170.420.558100
2.94-3.0512.60.29723180.9930.9980.0860.310.615100
3.05-3.1912.50.23223000.9940.9980.0680.2420.641100
3.19-3.3612.40.18422930.9960.9990.0540.1920.684100
3.36-3.5712.30.14123260.9960.9990.0420.1470.76100
3.57-3.85120.10723220.9970.9990.0320.1120.945100
3.85-4.2312.40.08923420.9970.9990.0260.0931.085100
4.23-4.8512.60.08223490.9980.9990.0240.0861.253100
4.85-6.112.30.08323780.9980.9990.0240.0861.309100
6.1-5011.60.06325030.9970.9990.0190.0661.37399.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.63 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1994 4.64 %
Rwork0.1871 --
obs0.1891 42958 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 32 267 4177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084012
X-RAY DIFFRACTIONf_angle_d0.8435435
X-RAY DIFFRACTIONf_dihedral_angle_d9.178530
X-RAY DIFFRACTIONf_chiral_restr0.048566
X-RAY DIFFRACTIONf_plane_restr0.007703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.3251060.33652224X-RAY DIFFRACTION71
2.31-2.370.41171190.31372469X-RAY DIFFRACTION79
2.37-2.440.42421360.31122714X-RAY DIFFRACTION88
2.44-2.520.2481420.26932812X-RAY DIFFRACTION90
2.52-2.610.30081440.24622864X-RAY DIFFRACTION92
2.61-2.710.28771360.23122927X-RAY DIFFRACTION94
2.71-2.840.27241440.22672998X-RAY DIFFRACTION96
2.84-2.990.29131410.23113004X-RAY DIFFRACTION96
2.99-3.170.26781490.20733065X-RAY DIFFRACTION98
3.18-3.420.26381510.19723088X-RAY DIFFRACTION99
3.42-3.760.22951520.16883133X-RAY DIFFRACTION99
3.76-4.310.16961490.1413165X-RAY DIFFRACTION99
4.31-5.420.16271590.13923203X-RAY DIFFRACTION100
5.43-48.630.19551660.15893298X-RAY DIFFRACTION99

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