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- PDB-8doh: Dehaloperoxidase B in complex with Bisphenol F -

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Basic information

Entry
Database: PDB / ID: 8doh
TitleDehaloperoxidase B in complex with Bisphenol F
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / dehaloperoxidase B / heme peroxidase / peroxigenase / oxygen binding / heme cofactor / oxidorductase
Function / homology
Function and homology information


oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 4,4'-methylenediphenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
Authorsde Serrano, V.S. / Yun, D. / Ghiladi, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Oxidation of bisphenol A (BPA) and related compounds by the multifunctional catalytic globin dehaloperoxidase.
Authors: Yun, D. / de Serrano, V. / Ghiladi, R.A.
History
DepositionJul 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,93511
Polymers30,8292
Non-polymers2,1069
Water3,369187
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6117
Polymers15,4141
Non-polymers1,1976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3234
Polymers15,4141
Non-polymers9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.672, 67.281, 67.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dehaloperoxidase B


Mass: 15414.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-T0U / 4,4'-methylenediphenol / Bisphenol F


Mass: 200.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, Ammonium Sulfate, Sodium Cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→37.56 Å / Num. obs: 34127 / % possible obs: 98.81 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Net I/σ(I): 23.45
Reflection shellResolution: 1.75→1.79 Å / Num. unique obs: 1803 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.75→37.298 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.375 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2197 1397 4.994 %
Rwork0.1697 26576 -
all0.172 --
obs-27973 98.806 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.856 Å20 Å20 Å2
2---0.179 Å20 Å2
3----0.677 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 143 187 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132814
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152517
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.73881
X-RAY DIFFRACTIONr_angle_other_deg1.6271.6245834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7675372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19523.077156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.781518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023475
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02741
X-RAY DIFFRACTIONr_nbd_refined0.2550.2828
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22387
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21350
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2189
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.140.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2910.226
X-RAY DIFFRACTIONr_nbd_other0.2540.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0950.21
X-RAY DIFFRACTIONr_mcbond_it1.0191.4421316
X-RAY DIFFRACTIONr_mcbond_other1.0131.4411315
X-RAY DIFFRACTIONr_mcangle_it1.5312.1581703
X-RAY DIFFRACTIONr_mcangle_other1.5332.1591704
X-RAY DIFFRACTIONr_scbond_it1.6911.7191498
X-RAY DIFFRACTIONr_scbond_other1.6861.7071487
X-RAY DIFFRACTIONr_scangle_it2.5912.5062157
X-RAY DIFFRACTIONr_scangle_other2.5842.4872140
X-RAY DIFFRACTIONr_lrange_it6.59118.9093645
X-RAY DIFFRACTIONr_lrange_other6.55318.7013614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7920.38930.3361803X-RAY DIFFRACTION91.905
1.792-1.8410.3021020.2511917X-RAY DIFFRACTION99.2625
1.841-1.8950.271860.2111818X-RAY DIFFRACTION99.6337
1.895-1.9530.2371000.1861806X-RAY DIFFRACTION99.7384
1.953-2.0170.2431150.1711727X-RAY DIFFRACTION99.9457
2.017-2.0870.216740.1681706X-RAY DIFFRACTION99.7199
2.087-2.1660.231920.1551632X-RAY DIFFRACTION100
2.166-2.2540.226880.1561588X-RAY DIFFRACTION99.8213
2.254-2.3540.227630.1571512X-RAY DIFFRACTION99.6835
2.354-2.4690.202840.1371443X-RAY DIFFRACTION100
2.469-2.6020.205630.1441406X-RAY DIFFRACTION99.932
2.602-2.7590.209690.1451298X-RAY DIFFRACTION100
2.759-2.9490.181710.1431245X-RAY DIFFRACTION99.9241
2.949-3.1850.212470.171175X-RAY DIFFRACTION99.9182
3.185-3.4870.213740.1721048X-RAY DIFFRACTION99.4681
3.487-3.8960.217450.162968X-RAY DIFFRACTION98.4451
3.896-4.4940.177450.145858X-RAY DIFFRACTION97.6216
4.494-5.4910.251470.177702X-RAY DIFFRACTION96.5206
5.491-7.7150.229240.212583X-RAY DIFFRACTION96.0443
7.715-37.2980.162150.212341X-RAY DIFFRACTION91.9897
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13860.3781-0.1571.234-0.83261.0506-0.0444-0.0403-0.0057-0.1105-0.1057-0.08780.07460.02160.15020.07310.01320.01130.01890.00460.03155.8243-2.339321.2887
20.3131-0.02740.03490.6189-0.17840.7317-0.01270.0279-0.01210.03180.0321-0.009-0.0183-0.0378-0.01940.07210.0090.00520.0260.00520.0031-21.3501-5.032419.2334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

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