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- PDB-8doj: Dehaloperoxidase B in complex with 3,3'-Biphenol -

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Basic information

Entry
Database: PDB / ID: 8doj
TitleDehaloperoxidase B in complex with 3,3'-Biphenol
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
PROTOPORPHYRIN IX CONTAINING FE / (1P)-[1,1'-biphenyl]-3,3'-diol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)32,6249
Polymers30,8292
Non-polymers1,7957
Water4,125229
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5016
Polymers15,4141
Non-polymers1,0875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1233
Polymers15,4141
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.595, 67.374, 67.647
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, 236 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-T1I / (1P)-[1,1'-biphenyl]-3,3'-diol / 3,3'-Biphenol


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
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-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→33.85 Å / Num. obs: 62722 / % possible obs: 91.24 % / Redundancy: 3.4 % / CC1/2: 0.994 / Net I/σ(I): 27.88
Reflection shellResolution: 1.3→1.334 Å / Num. unique obs: 4592 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.3→33.846 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.233 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1889 3109 4.957 %
Rwork0.1455 59613 -
all0.148 --
obs-62722 91.24 %
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: 16.493 Å2
Baniso -1Baniso -2Baniso -3
1--1.641 Å20 Å2-0 Å2
2--1.149 Å20 Å2
3---0.492 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 122 229 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122729
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162372
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.6953760
X-RAY DIFFRACTIONr_angle_other_deg0.6631.5995588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.131018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70610478
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4610132
X-RAY DIFFRACTIONr_chiral_restr0.0940.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023347
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02603
X-RAY DIFFRACTIONr_nbd_refined0.2710.2693
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22151
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21332
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21325
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.219
X-RAY DIFFRACTIONr_nbd_other0.2030.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.226
X-RAY DIFFRACTIONr_mcbond_it2.6421.5731290
X-RAY DIFFRACTIONr_mcbond_other2.6421.5731290
X-RAY DIFFRACTIONr_mcangle_it3.2352.3741665
X-RAY DIFFRACTIONr_mcangle_other3.2362.3761666
X-RAY DIFFRACTIONr_scbond_it4.691.9241439
X-RAY DIFFRACTIONr_scbond_other4.6961.9241432
X-RAY DIFFRACTIONr_scangle_it5.2162.7462073
X-RAY DIFFRACTIONr_scangle_other5.2192.7442062
X-RAY DIFFRACTIONr_lrange_it4.86527.333433
X-RAY DIFFRACTIONr_lrange_other4.75525.4423380
X-RAY DIFFRACTIONr_rigid_bond_restr6.335101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.3052720.28745920.28850160.9730.98296.96970.286
1.334-1.370.2932260.24744590.24948550.970.98496.49850.24
1.37-1.410.2932250.20643360.2147650.9620.98595.71880.195
1.41-1.4530.2552000.17341670.17746170.970.98794.58520.158
1.453-1.5010.2282110.15939040.16344920.9740.98991.60730.141
1.501-1.5530.2072010.13538870.13943400.9720.99194.19360.123
1.553-1.6120.21780.13237330.13542000.9740.99193.1190.12
1.612-1.6770.1732060.12135510.12440630.9830.99392.46860.111
1.677-1.7520.1641530.12234140.12438710.9830.99392.14670.114
1.752-1.8370.1811350.12332290.12637210.9830.99390.40580.117
1.837-1.9360.181770.12429930.12735610.980.99289.01990.118
1.936-2.0530.1781270.12427170.12633520.980.99284.84490.122
2.053-2.1940.1671340.12726790.12931520.9830.99289.24490.128
2.194-2.3690.1741320.12324980.12629580.9820.99288.91140.128
2.369-2.5940.1481150.11223170.11327590.9860.99388.14790.123
2.594-2.8980.181090.1320710.13324900.9790.98987.55020.147
2.898-3.3430.171020.14617610.14822030.9790.98784.56650.167
3.343-4.0840.1791030.13914530.14218920.9810.98882.2410.165
4.084-5.7340.18750.17911530.17915040.9790.98581.64890.226
5.734-33.8460.268280.2326970.2339060.9610.97380.02210.296

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