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

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Basic information

Entry
Database: PDB / ID: 6vdr
TitleCrystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-bromophenol
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 domain profile. / Globin-like superfamily
Similarity search - Domain/homology
4-BROMOPHENOL / FE(III) DEUTEROPORPHYRIN IX / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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

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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)32,86814
Polymers30,8292
Non-polymers2,03912
Water2,270126
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3726
Polymers15,4141
Non-polymers9585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4968
Polymers15,4141
Non-polymers1,0827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.401, 67.641, 67.646
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 , 5 types, 138 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-BML / 4-BROMOPHENOL


Mass: 173.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5BrO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 126 / 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: 44.19 %
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: Jun 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→37.28 Å / Num. obs: 22564 / % possible obs: 97.56 % / Redundancy: 9.6 % / CC1/2: 0.997 / Net I/σ(I): 32.7
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 1224 / CC1/2: 0.997

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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: 1.87→37.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.724 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.205 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2502 1153 5.11 %
Rwork0.2035 --
all0.206 --
obs-21411 97.561 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.394 Å2
Baniso -1Baniso -2Baniso -3
1-2.306 Å20 Å20 Å2
2---1.04 Å20 Å2
3----1.266 Å2
Refinement stepCycle: LAST / Resolution: 1.87→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 128 126 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132772
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182463
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.7023805
X-RAY DIFFRACTIONr_angle_other_deg1.4091.6185777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9025368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07422.727154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45615501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6761519
X-RAY DIFFRACTIONr_chiral_restr0.1760.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023345
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02646
X-RAY DIFFRACTIONr_nbd_refined0.2320.2760
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22093
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21310
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21016
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2148
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1630.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.231
X-RAY DIFFRACTIONr_nbd_other0.2240.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2680.220
X-RAY DIFFRACTIONr_mcbond_it2.0272.8331306
X-RAY DIFFRACTIONr_mcbond_other2.0232.8321305
X-RAY DIFFRACTIONr_mcangle_it2.8644.2411692
X-RAY DIFFRACTIONr_mcangle_other2.8634.2421693
X-RAY DIFFRACTIONr_scbond_it2.7363.1431466
X-RAY DIFFRACTIONr_scbond_other2.5533.1291459
X-RAY DIFFRACTIONr_scangle_it3.9914.5932095
X-RAY DIFFRACTIONr_scangle_other3.9324.5752084
X-RAY DIFFRACTIONr_lrange_it5.49334.1943468
X-RAY DIFFRACTIONr_lrange_other5.45834.0863447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9180.323670.2761224X-RAY DIFFRACTION78.1004
1.918-1.9710.276710.2451390X-RAY DIFFRACTION90.8017
1.971-2.0280.31900.2361478X-RAY DIFFRACTION97.6339
2.028-2.090.362620.2141488X-RAY DIFFRACTION99.4227
2.09-2.1590.28790.211425X-RAY DIFFRACTION100
2.159-2.2340.242640.2051395X-RAY DIFFRACTION100
2.234-2.3180.351660.2081357X-RAY DIFFRACTION100
2.318-2.4130.276760.211263X-RAY DIFFRACTION100
2.413-2.520.276520.21265X-RAY DIFFRACTION100
2.52-2.6430.327460.21200X-RAY DIFFRACTION100
2.643-2.7850.269800.1831111X-RAY DIFFRACTION100
2.785-2.9530.248470.1721102X-RAY DIFFRACTION100
2.953-3.1560.241670.206990X-RAY DIFFRACTION100
3.156-3.4080.26560.201951X-RAY DIFFRACTION100
3.408-3.7310.224600.194859X-RAY DIFFRACTION100
3.731-4.1690.204370.181809X-RAY DIFFRACTION100
4.169-4.8080.214480.19705X-RAY DIFFRACTION100
4.808-5.8730.19390.224607X-RAY DIFFRACTION100
5.873-8.2440.36280.23491X-RAY DIFFRACTION100
8.244-37.280.168180.218299X-RAY DIFFRACTION98.7539

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