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- PDB-7sjf: Structure of Dehaloperoxidase B in Complex with Thymol -

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Basic information

Entry
Database: PDB / ID: 7sjf
TitleStructure of Dehaloperoxidase B in Complex with Thymol
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
PROTOPORPHYRIN IX CONTAINING FE / 5-METHYL-2-(1-METHYLETHYL)PHENOL / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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

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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)32,6479
Polymers30,8292
Non-polymers1,8187
Water1,13563
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3695
Polymers15,4141
Non-polymers9554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2774
Polymers15,4141
Non-polymers8633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.316, 66.898, 67.615
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 , 5 types, 70 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IPB / 5-METHYL-2-(1-METHYLETHYL)PHENOL / Thymol


Mass: 150.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsLigand IPB occupies density that is close to the position of H55 in its alternate conformation. The ...Ligand IPB 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / 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
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.6444
pseudo-merohedral22-H, -L, -K20.3556
ReflectionResolution: 1.81→37.344 Å / Num. obs: 20141 / % possible obs: 83.07 % / Redundancy: 4.2 % / CC1/2: 0.998 / Net I/σ(I): 22.1
Reflection shellResolution: 1.811→1.858 Å / Num. unique obs: 1123 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.96→37.344 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.888 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2912 838 5.056 %
Rwork0.2066 15737 -
all0.211 --
obs-16575 81.9 %
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: 31.51 Å2
Baniso -1Baniso -2Baniso -3
1-19.955 Å20 Å20 Å2
2---13.75 Å2-0 Å2
3----6.205 Å2
Refinement stepCycle: LAST / Resolution: 1.96→37.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 124 63 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132755
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152509
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.6953803
X-RAY DIFFRACTIONr_angle_other_deg1.4411.6475819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4285369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23823.179151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60615491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.651518
X-RAY DIFFRACTIONr_chiral_restr0.10.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023521
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02717
X-RAY DIFFRACTIONr_nbd_refined0.2660.2859
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.22618
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21304
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.221
X-RAY DIFFRACTIONr_nbd_other0.190.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.216
X-RAY DIFFRACTIONr_mcbond_it1.652.6171298
X-RAY DIFFRACTIONr_mcbond_other1.6492.6181299
X-RAY DIFFRACTIONr_mcangle_it2.3833.9261680
X-RAY DIFFRACTIONr_mcangle_other2.3843.9271681
X-RAY DIFFRACTIONr_scbond_it1.7352.8711457
X-RAY DIFFRACTIONr_scbond_other1.7152.8691450
X-RAY DIFFRACTIONr_scangle_it2.5044.2792102
X-RAY DIFFRACTIONr_scangle_other2.4784.2762091
X-RAY DIFFRACTIONr_lrange_it6.22432.9193478
X-RAY DIFFRACTIONr_lrange_other6.22532.8953466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0110.374440.33779X-RAY DIFFRACTION55.7211
2.011-2.0660.557730.3741152X-RAY DIFFRACTION86.3284
2.066-2.1260.433690.3431132X-RAY DIFFRACTION86.4029
2.126-2.1910.349720.281127X-RAY DIFFRACTION88.6179
2.191-2.2630.43520.2741034X-RAY DIFFRACTION81.7771
2.263-2.3420.43360.2541059X-RAY DIFFRACTION86.8358
2.342-2.430.377580.223996X-RAY DIFFRACTION84.9315
2.43-2.5290.332590.209930X-RAY DIFFRACTION84.1702
2.529-2.6410.325500.202920X-RAY DIFFRACTION84.1284
2.641-2.770.254220.198862X-RAY DIFFRACTION82.1561
2.77-2.9190.195450.205811X-RAY DIFFRACTION81.1374
2.919-3.0950.234490.216749X-RAY DIFFRACTION80.6876
3.095-3.3080.24320.206727X-RAY DIFFRACTION81.877
3.308-3.5710.261300.191635X-RAY DIFFRACTION74.8874
3.571-3.910.24250.171619X-RAY DIFFRACTION80.5
3.91-4.3680.262350.146586X-RAY DIFFRACTION83.5801
4.368-5.0370.209370.161523X-RAY DIFFRACTION84.4646
5.037-6.1510.423210.2482X-RAY DIFFRACTION89.1844
6.151-8.6270.157140.175389X-RAY DIFFRACTION88.1838
8.627-37.3440.247150.164225X-RAY DIFFRACTION86.0215
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.22680.3783-0.31871.165-0.54130.4539-0.01520.0089-0.0699-0.083-0.0962-0.09260.0291-0.00420.11140.06050.0101-0.00180.08030.01570.0465.7954-2.39421.136
20.60970.0176-0.01820.5838-0.46210.5940.00620.02160.03920.01780.05330.04-0.0353-0.0633-0.05950.07500.01520.06550.00860.0102-21.29-4.843719.1348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

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