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

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Basic information

Entry
Database: PDB / ID: 6vdu
TitleCrystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate Trichlorophenol
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
FE(III) DEUTEROPORPHYRIN IX / DI(HYDROXYETHYL)ETHER / 2,4,6-trichlorophenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 1.1Oct 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 / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 25, 2024Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn / Item: _pdbx_entry_details.has_protein_modification

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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)32,89913
Polymers30,8292
Non-polymers2,07011
Water1,56787
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5998
Polymers15,4141
Non-polymers1,1847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3005
Polymers15,4141
Non-polymers8864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.174, 67.901, 67.905
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, 98 molecules

#2: Chemical ChemComp-FDE / FE(III) DEUTEROPORPHYRIN IX


Mass: 564.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.41 %
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: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→44.65 Å / Num. obs: 19407 / % possible obs: 98.47 % / Redundancy: 4.7 % / CC1/2: 0.997 / Net I/σ(I): 20.8
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 1254 / CC1/2: 0.777

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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: 3IXF

3ixf


Resolution: 1.98→44.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.92 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2608 1040 5.359 %
Rwork0.1971 --
all0.201 --
obs-19407 98.473 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.948 Å20 Å2-0 Å2
2---0.639 Å20 Å2
3----0.309 Å2
Refinement stepCycle: LAST / Resolution: 1.98→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 131 87 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132592
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182289
X-RAY DIFFRACTIONr_angle_refined_deg2.3281.7013566
X-RAY DIFFRACTIONr_angle_other_deg1.5541.6175351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3295347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37322.836134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05315446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9211516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023115
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02591
X-RAY DIFFRACTIONr_nbd_refined0.2490.2640
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22040
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21254
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21030
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.221
X-RAY DIFFRACTIONr_nbd_other0.2150.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.217
X-RAY DIFFRACTIONr_mcbond_it1.6652.2261242
X-RAY DIFFRACTIONr_mcbond_other1.652.2241241
X-RAY DIFFRACTIONr_mcangle_it2.6063.3091599
X-RAY DIFFRACTIONr_mcangle_other2.6093.311600
X-RAY DIFFRACTIONr_scbond_it2.3332.8361350
X-RAY DIFFRACTIONr_scbond_other2.3172.8341343
X-RAY DIFFRACTIONr_scangle_it3.6024.2491947
X-RAY DIFFRACTIONr_scangle_other3.5784.2431936
X-RAY DIFFRACTIONr_lrange_it6.04428.7183155
X-RAY DIFFRACTIONr_lrange_other6.01728.6583147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.0290.29800.2521254X-RAY DIFFRACTION93.352
2.029-2.0850.308640.2311318X-RAY DIFFRACTION99.2103
2.085-2.1450.235610.2091302X-RAY DIFFRACTION99.7074
2.145-2.2110.255750.21231X-RAY DIFFRACTION99.6947
2.211-2.2830.255510.2031216X-RAY DIFFRACTION99.3726
2.283-2.3630.332840.2061151X-RAY DIFFRACTION99.5165
2.363-2.4520.276720.1771115X-RAY DIFFRACTION99.5805
2.452-2.5520.202590.1611090X-RAY DIFFRACTION99.5667
2.552-2.6650.183450.1791071X-RAY DIFFRACTION99.3767
2.665-2.7950.377480.1971007X-RAY DIFFRACTION99.7164
2.795-2.9460.284710.19943X-RAY DIFFRACTION99.5093
2.946-3.1240.238360.213921X-RAY DIFFRACTION99.2739
3.124-3.3380.336430.211855X-RAY DIFFRACTION98.7899
3.338-3.6040.234530.213791X-RAY DIFFRACTION98.5981
3.604-3.9460.234570.188715X-RAY DIFFRACTION98.3439
3.946-4.4080.284390.165667X-RAY DIFFRACTION98.7413
4.408-5.0830.258330.171601X-RAY DIFFRACTION97.9907
5.083-6.2080.167370.236498X-RAY DIFFRACTION96.5704
6.208-8.7070.316190.213398X-RAY DIFFRACTION93.7079
8.707-44.650.355130.2223X-RAY DIFFRACTION87.0849
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)
10.1282-0.21350.23261.50630.41361.0035-0.0188-0.0345-0.0004-0.1280.0655-0.0248-0.1183-0.0455-0.04670.0545-0.01790.00580.0521-0.01940.0513-11.0246-2.20415.6024
20.48160.5862-0.5711.3165-0.75062.7116-0.00670.0061-0.19830.0080.2993-0.2361-0.18030.0472-0.29260.0173-0.00070.05010.1464-0.0210.2177-4.6754-10.074613.3516
30.1147-0.1650.26470.74010.24511.4211-0.00610.00380.04030.0878-0.054-0.07040.1087-0.01450.06010.0427-0.01190.01340.0625-0.01550.0507-33.3391-1.370514.5952
40.29730.31240.24462.2136-0.4061.10820.04820.07040.08770.1812-0.29190.0820.0257-0.10770.24370.0352-0.02720.03420.2149-0.05230.0783-39.847-3.66937.1172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 90
2X-RAY DIFFRACTION2ALLA91 - 137
3X-RAY DIFFRACTION3ALLB1 - 87
4X-RAY DIFFRACTION4ALLB88 - 137

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