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- PDB-6ong: Dehaloperoxidate B in complex with substrate 4-F-cresol -

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Basic information

Entry
Database: PDB / ID: 6ong
TitleDehaloperoxidate B in complex with substrate 4-F-cresol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / peroxidase activity / oxygen binding / 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 / 4-fluoro-2-methylphenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Malewschik, T. / McGuire, A.
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 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,13317
Polymers30,8292
Non-polymers2,30415
Water4,810267
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4116
Polymers15,4141
Non-polymers9975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,72211
Polymers15,4141
Non-polymers1,30710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.084, 67.237, 67.825
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 , 5 types, 282 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-MWM / 4-fluoro-2-methylphenol


Mass: 126.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7FO / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#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 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulphate, Na 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 MX300HE / 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: 1.42→44.55 Å / Num. obs: 49099 / % possible obs: 99.97 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Biso Wilson estimate: 8 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.06 / Rrim(I) all: 0.06 / Χ2: 0.79 / Net I/σ(I): 10.4
Reflection shellResolution: 1.42→1.457 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3539 / CC1/2: 0.91 / Rpim(I) all: 0.15 / Rrim(I) all: 0.36 / % possible all: 99.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→44.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.431 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.014 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18378 2574 5 %RANDOM
Rwork0.14516 ---
obs0.14702 49099 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.522 Å2
Baniso -1Baniso -2Baniso -3
1-8.24 Å20 Å20 Å2
2---4.06 Å2-0 Å2
3----4.18 Å2
Refinement stepCycle: 1 / Resolution: 1.42→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 152 267 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133081
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182733
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.7044235
X-RAY DIFFRACTIONr_angle_other_deg1.5711.6256433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.395410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13922.989174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5415569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9731521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023728
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02711
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_it0.9440.8281430
X-RAY DIFFRACTIONr_mcbond_other0.9430.8271429
X-RAY DIFFRACTIONr_mcangle_it1.2571.2511861
X-RAY DIFFRACTIONr_mcangle_other1.2571.2511862
X-RAY DIFFRACTIONr_scbond_it1.2091.0261651
X-RAY DIFFRACTIONr_scbond_other1.1931.0161636
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4341.4422326
X-RAY DIFFRACTIONr_long_range_B_refined2.34910.6983994
X-RAY DIFFRACTIONr_long_range_B_other2.23610.4843945
X-RAY DIFFRACTIONr_rigid_bond_restr1.16135814
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 215 -
Rwork0.172 3539 -
obs--99.84 %

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