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- PDB-6onr: Dehaloperoxidase B in complex with substrate 4-methyl-cresol -

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Basic information

Entry
Database: PDB / ID: 6onr
TitleDehaloperoxidase B in complex with substrate 4-methyl-cresol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxydase / peroxygenase / heme cofactor
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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 2,4-dimethylphenol / DI(HYDROXYETHYL)ETHER / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Malewschik, T.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants.
Authors: Malewschik, T. / de Serrano, V. / McGuire, A.H. / Ghiladi, R.A.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,03916
Polymers30,8292
Non-polymers2,21014
Water6,233346
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5949
Polymers15,4141
Non-polymers1,1798
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4457
Polymers15,4141
Non-polymers1,0316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.206, 67.402, 67.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / Plasmid: pET16b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS AG / References: UniProt: Q9NAV7

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Non-polymers , 6 types, 360 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-N0D / 2,4-dimethylphenol


Mass: 122.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulphate, 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: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→37.22 Å / Num. obs: 56853 / % possible obs: 99.45 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.046 / Χ2: 1.012 / Net I/σ(I): 35.3
Reflection shellResolution: 1.35→1.385 Å / Redundancy: 2.9 % / Num. unique obs: 4091 / CC1/2: 0.82 / Rpim(I) all: 0.243 / Rrim(I) all: 0.438 / Χ2: 0.707 / % possible all: 96.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.35→37.22 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.052 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16096 3064 5.1 %RANDOM
Rwork0.12567 ---
obs0.1275 56853 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0 Å2
2---1.85 Å20 Å2
3---1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.35→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 149 346 2652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182687
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.7034107
X-RAY DIFFRACTIONr_angle_other_deg1.5861.626305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77423.086162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60915547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0441519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023624
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02689
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5081.3091393
X-RAY DIFFRACTIONr_mcbond_other1.5081.3081392
X-RAY DIFFRACTIONr_mcangle_it1.9241.981818
X-RAY DIFFRACTIONr_mcangle_other1.9241.981819
X-RAY DIFFRACTIONr_scbond_it1.9761.5551593
X-RAY DIFFRACTIONr_scbond_other1.9771.5561586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2932.2282254
X-RAY DIFFRACTIONr_long_range_B_refined3.24116.9733873
X-RAY DIFFRACTIONr_long_range_B_other2.92616.3773791
X-RAY DIFFRACTIONr_rigid_bond_restr4.08535673
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 185 -
Rwork0.203 4091 -
obs--96.94 %

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