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- PDB-8dog: Dehaloperoxidase B in complex with Bisphenol E -

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Basic information

Entry
Database: PDB / ID: 8dog
TitleDehaloperoxidase B in complex with Bisphenol E
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-like superfamily
Similarity search - Domain/homology
4-[1-(4-hydroxyphenyl)ethyl]phenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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)32,96311
Polymers30,8292
Non-polymers2,1349
Water4,702261
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6257
Polymers15,4141
Non-polymers1,2116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3374
Polymers15,4141
Non-polymers9233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.827, 67.344, 67.656
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 (E. coli) / Strain (production host): BL(21) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 270 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-H48 / 4-[1-(4-hydroxyphenyl)ethyl]phenol


Mass: 214.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion / 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: 1.48→37.58 Å / Num. obs: 46747 / % possible obs: 99.24 % / Redundancy: 4.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.03 / Net I/σ(I): 24
Reflection shellResolution: 1.48→1.518 Å / Num. unique obs: 3013 / CC1/2: 0.76

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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: 1.48→37.578 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.95 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.172 2234 4.779 %
Rwork0.1261 44513 -
all0.128 --
obs-46747 99.24 %
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: 14.421 Å2
Baniso -1Baniso -2Baniso -3
1--1.393 Å2-0 Å20 Å2
2--1.061 Å2-0 Å2
3---0.332 Å2
Refinement stepCycle: LAST / Resolution: 1.48→37.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 145 261 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132762
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152470
X-RAY DIFFRACTIONr_angle_refined_deg2.091.6973814
X-RAY DIFFRACTIONr_angle_other_deg1.7061.6235729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47223.333147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4641515
X-RAY DIFFRACTIONr_chiral_restr0.1120.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023401
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02717
X-RAY DIFFRACTIONr_nbd_refined0.270.2747
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22282
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21340
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2197
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.219
X-RAY DIFFRACTIONr_nbd_other0.1950.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1490.21
X-RAY DIFFRACTIONr_mcbond_it2.1471.2321302
X-RAY DIFFRACTIONr_mcbond_other2.1391.2311301
X-RAY DIFFRACTIONr_mcangle_it2.5521.8621684
X-RAY DIFFRACTIONr_mcangle_other2.5511.8631685
X-RAY DIFFRACTIONr_scbond_it3.5191.5451460
X-RAY DIFFRACTIONr_scbond_other3.5151.5411449
X-RAY DIFFRACTIONr_scangle_it3.9432.1912109
X-RAY DIFFRACTIONr_scangle_other3.9392.1812092
X-RAY DIFFRACTIONr_lrange_it3.82616.0943540
X-RAY DIFFRACTIONr_lrange_other3.67515.6583482
X-RAY DIFFRACTIONr_rigid_bond_restr5.04335232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5180.3981740.2833013X-RAY DIFFRACTION92.5646
1.518-1.5590.2761560.2253113X-RAY DIFFRACTION98.0504
1.559-1.6040.2141470.1633099X-RAY DIFFRACTION99.8155
1.604-1.6540.1831400.1213030X-RAY DIFFRACTION99.9055
1.654-1.7080.21360.1032912X-RAY DIFFRACTION100
1.708-1.7680.1721570.1032848X-RAY DIFFRACTION100
1.768-1.8340.1751550.1042706X-RAY DIFFRACTION99.9651
1.834-1.9090.161250.0972655X-RAY DIFFRACTION100
1.909-1.9940.1611410.0962500X-RAY DIFFRACTION99.9622
1.994-2.0910.1631380.12419X-RAY DIFFRACTION99.9609
2.091-2.2040.1591150.1042311X-RAY DIFFRACTION100
2.204-2.3370.171950.12215X-RAY DIFFRACTION99.8703
2.337-2.4980.1451040.0972052X-RAY DIFFRACTION100
2.498-2.6980.145660.1111975X-RAY DIFFRACTION99.951
2.698-2.9540.155900.1131784X-RAY DIFFRACTION99.9467
2.954-3.3010.149750.1181624X-RAY DIFFRACTION99.9412
3.301-3.8090.181820.1291447X-RAY DIFFRACTION100
3.809-4.6580.119580.1261233X-RAY DIFFRACTION100
4.658-6.5560.158460.199985X-RAY DIFFRACTION100
6.556-37.5780.212340.21592X-RAY DIFFRACTION99.3651

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