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- PDB-6vdx: Crystal Structure of Dehaloperoxidase B in Complex with cofactor ... -

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Basic information

Entry
Database: PDB / ID: 6vdx
TitleCrystal Structure of Dehaloperoxidase B in Complex with cofactor Manganese(III)- Porphyrin and Substrate Trichlorophenol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / peroxidase activity / 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 MN / DI(HYDROXYETHYL)ETHER / 2,4,6-trichlorophenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / McGuire, A. / Malewschik, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
Authors: McGuire, A.H. / Petit, A.R. / Kang, J. / Malewschik, T. / de Serrano, V. / Carey, L.M. / Ghiladi, R.A.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: 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)33,09814
Polymers30,8292
Non-polymers2,26912
Water3,351186
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6508
Polymers15,4141
Non-polymers1,2357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4486
Polymers15,4141
Non-polymers1,0335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.365, 67.585, 67.626
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) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS / References: UniProt: Q9NAV7

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Non-polymers , 6 types, 198 molecules

#2: Chemical ChemComp-T6C / 2,4,6-trichlorophenol


Mass: 197.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H3Cl3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MNR / PROTOPORPHYRIN IX CONTAINING MN


Mass: 615.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32MnN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium Sulphate MPEG 2000, 29-33%

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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: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→44.642 Å / Num. obs: 41678 / % possible obs: 99.83 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 1 / Net I/σ(I): 28.1
Reflection shellResolution: 1.53→1.56 Å / Num. unique obs: 2538 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3xif

3xif


Resolution: 1.53→44.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.584 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2367 2150 5.159 %
Rwork0.1645 --
all0.168 --
obs-41678 99.82 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.577 Å2
Baniso -1Baniso -2Baniso -3
1--1.917 Å2-0 Å2-0 Å2
2---0.551 Å20 Å2
3---2.468 Å2
Refinement stepCycle: LAST / Resolution: 1.53→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 144 187 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132818
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182457
X-RAY DIFFRACTIONr_angle_refined_deg2.5831.73887
X-RAY DIFFRACTIONr_angle_other_deg1.611.6225760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58623.137153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74515488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3851517
X-RAY DIFFRACTIONr_chiral_restr0.1040.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023459
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02662
X-RAY DIFFRACTIONr_nbd_refined0.240.2783
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22223
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21375
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2180
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.230
X-RAY DIFFRACTIONr_nbd_other0.2660.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3050.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1930.21
X-RAY DIFFRACTIONr_mcbond_it3.4181.9121339
X-RAY DIFFRACTIONr_mcbond_other3.4171.9111338
X-RAY DIFFRACTIONr_mcangle_it4.2352.8911747
X-RAY DIFFRACTIONr_mcangle_other4.2342.8921748
X-RAY DIFFRACTIONr_scbond_it4.1932.1121479
X-RAY DIFFRACTIONr_scbond_other4.1922.1081465
X-RAY DIFFRACTIONr_scangle_it5.1583.0912126
X-RAY DIFFRACTIONr_scangle_other5.1533.0832108
X-RAY DIFFRACTIONr_lrange_it5.51323.7833623
X-RAY DIFFRACTIONr_lrange_other5.4923.6013593
X-RAY DIFFRACTIONr_rigid_bond_restr7.87135275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.3751940.2282831X-RAY DIFFRACTION99.7034
1.57-1.6130.2971460.1982813X-RAY DIFFRACTION99.9325
1.613-1.6590.2751700.1762725X-RAY DIFFRACTION100
1.659-1.710.2981390.1732642X-RAY DIFFRACTION100
1.71-1.7660.2541150.1562616X-RAY DIFFRACTION100
1.766-1.8280.2471230.1592520X-RAY DIFFRACTION99.9622
1.828-1.8970.2611210.1632405X-RAY DIFFRACTION100
1.897-1.9750.2281050.1382351X-RAY DIFFRACTION100
1.975-2.0620.2271260.1492229X-RAY DIFFRACTION100
2.062-2.1630.1951130.1352156X-RAY DIFFRACTION99.9559
2.163-2.2790.2491240.1532028X-RAY DIFFRACTION99.9536
2.279-2.4170.188940.1311955X-RAY DIFFRACTION99.9512
2.417-2.5840.2021030.1461839X-RAY DIFFRACTION99.8458
2.584-2.790.2141060.1431669X-RAY DIFFRACTION100
2.79-3.0550.215790.171578X-RAY DIFFRACTION99.7592
3.055-3.4140.263590.1881446X-RAY DIFFRACTION99.4055
3.414-3.9390.202750.1651265X-RAY DIFFRACTION99.0392
3.939-4.8160.223680.151073X-RAY DIFFRACTION98.8735
4.816-6.7770.318430.223880X-RAY DIFFRACTION99.3541
6.777-44.640.26450.23493X-RAY DIFFRACTION97.8182

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