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- PDB-7sjg: Structure of Dehaloperoxidase B in Complex with Thymoquinone -

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Basic information

Entry
Database: PDB / ID: 7sjg
TitleStructure of Dehaloperoxidase B in Complex with Thymoquinone
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding
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
2-methyl-5-(propan-2-yl)benzene-1,4-diol / Chem-9J9 / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Malewschik, T. / Yun, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes
Authors: Malewschick, T. / Yun, D. / de Serrano, V. / Ghiladi, R.A.
History
DepositionOct 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)33,80418
Polymers30,8292
Non-polymers2,97516
Water3,747208
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,16411
Polymers15,4141
Non-polymers1,75010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6407
Polymers15,4141
Non-polymers1,2256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.358, 67.565, 67.825
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 (bacteria) / Variant (production host): Gold(DE3) / References: UniProt: Q9NAV7

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Non-polymers , 6 types, 224 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-9J9 / (6R)-4-hydroxy-6-methyl-3-(propan-2-yl)cyclohexa-2,4-dien-1-one


Mass: 166.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-9IX / 2-methyl-5-(propan-2-yl)benzene-1,4-diol / Thymoquinone


Mass: 166.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsLigand 9J9 occupies density that is close to the position of H55 in its alternate conformation. The ...Ligand 9J9 occupies density that is close to the position of H55 in its alternate conformation. The occupancies of the alternate conformations reflect the fact. In the fraction where the ligand is bound, reflected by the occupancy of the ligand, H55 is in the conformation facing outside of the distal side of the heme pocket, with the same occupancy as the bound ligand. When the ligand is not bound, H55 can occupy the inside conformation, also reflected by its occupancy.

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulfate, 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 MX300-HS / Detector: CCD / Date: Jul 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.2 Å / Num. obs: 53478 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 17.1
Reflection shellResolution: 1.4→1.436 Å / Num. unique obs: 3750 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.4→44.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.415 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1949 2686 5.023 %
Rwork0.1424 50792 -
all0.145 --
obs-53478 99.923 %
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: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.294 Å20 Å2-0 Å2
2---3.379 Å20 Å2
3---1.085 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 204 208 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132978
X-RAY DIFFRACTIONr_bond_other_d0.0040.0152689
X-RAY DIFFRACTIONr_angle_refined_deg2.2581.6974112
X-RAY DIFFRACTIONr_angle_other_deg1.7041.666244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05123.671158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13415517
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.17152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5731516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023896
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02748
X-RAY DIFFRACTIONr_nbd_refined0.2950.2927
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.22661
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21414
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.270.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3060.240
X-RAY DIFFRACTIONr_nbd_other0.2960.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.229
X-RAY DIFFRACTIONr_mcbond_it3.7141.821385
X-RAY DIFFRACTIONr_mcbond_other3.7131.8211386
X-RAY DIFFRACTIONr_mcangle_it4.5012.7551810
X-RAY DIFFRACTIONr_mcangle_other4.5052.7581811
X-RAY DIFFRACTIONr_scbond_it8.8842.3721593
X-RAY DIFFRACTIONr_scbond_other8.9012.3751586
X-RAY DIFFRACTIONr_scangle_it9.9953.3872281
X-RAY DIFFRACTIONr_scangle_other10.0113.3872269
X-RAY DIFFRACTIONr_lrange_it8.96825.6163830
X-RAY DIFFRACTIONr_lrange_other8.92225.4463798
X-RAY DIFFRACTIONr_rigid_bond_restr5.31435667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2791660.2383750X-RAY DIFFRACTION99.8725
1.436-1.4760.2652060.2093576X-RAY DIFFRACTION99.9736
1.476-1.5180.2291920.1833517X-RAY DIFFRACTION100
1.518-1.5650.2211850.1643414X-RAY DIFFRACTION99.9722
1.565-1.6160.1881460.143335X-RAY DIFFRACTION100
1.616-1.6730.2261790.143200X-RAY DIFFRACTION100
1.673-1.7360.211580.1343111X-RAY DIFFRACTION99.9694
1.736-1.8070.1991640.1312985X-RAY DIFFRACTION100
1.807-1.8870.2221880.1252846X-RAY DIFFRACTION100
1.887-1.9790.1791630.122719X-RAY DIFFRACTION99.896
1.979-2.0860.1931260.1182638X-RAY DIFFRACTION99.9638
2.086-2.2120.1751280.1152472X-RAY DIFFRACTION99.9616
2.212-2.3650.1621290.1062350X-RAY DIFFRACTION100
2.365-2.5530.1751270.1132180X-RAY DIFFRACTION99.9567
2.553-2.7960.193970.1292042X-RAY DIFFRACTION100
2.796-3.1250.181150.1361807X-RAY DIFFRACTION99.6888
3.125-3.6060.179700.1441660X-RAY DIFFRACTION99.9422
3.606-4.410.179710.1381382X-RAY DIFFRACTION99.7255
4.41-6.2110.225500.1811124X-RAY DIFFRACTION99.7451
6.211-44.20.199250.232670X-RAY DIFFRACTION98.1638

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