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- PDB-6onz: Dehaloperoxidase B in complex with substtrate 4-nitro-cresol -

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Basic information

Entry
Database: PDB / ID: 6onz
TitleDehaloperoxidase B in complex with substtrate 4-nitro-cresol
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 / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 2-methyl-4-nitrophenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Malewschik, T.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants.
Authors: Malewschik, T. / de Serrano, V. / McGuire, A.H. / Ghiladi, R.A.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)33,21518
Polymers30,8292
Non-polymers2,38616
Water3,837213
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,74911
Polymers15,4141
Non-polymers1,33410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4667
Polymers15,4141
Non-polymers1,0526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.600, 67.730, 67.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / Plasmid: pET16b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Gold(DE3)pLysS AG / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 229 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-MYJ / 2-methyl-4-nitrophenol


Mass: 153.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulphate, sodium 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: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37.11 Å / Num. obs: 23857 / % possible obs: 97.78 % / Observed criterion σ(I): 1.5 / Redundancy: 5.4 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.916 / Rpim(I) all: 0.052 / Rrim(I) all: 0.091 / Χ2: 0.84 / Net I/σ(I): 3.9
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1665 / CC1/2: 0.798 / Rpim(I) all: 0.294 / Rrim(I) all: 0.581 / Χ2: 0.61 / % possible all: 93.42

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.11 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2306 1281 5.1 %
Rwork0.1809 --
obs0.1833 25133 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 159 213 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052984
X-RAY DIFFRACTIONf_angle_d0.8294098
X-RAY DIFFRACTIONf_dihedral_angle_d10.2562663
X-RAY DIFFRACTIONf_chiral_restr0.044396
X-RAY DIFFRACTIONf_plane_restr0.006551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87210.26141360.21692532X-RAY DIFFRACTION94
1.8721-1.95730.27051410.20382538X-RAY DIFFRACTION96
1.9573-2.06050.2351280.18972572X-RAY DIFFRACTION96
2.0605-2.18960.24761440.18492612X-RAY DIFFRACTION97
2.1896-2.35860.24531380.18352639X-RAY DIFFRACTION99
2.3586-2.59590.21521470.17692681X-RAY DIFFRACTION100
2.5959-2.97140.24561330.17172730X-RAY DIFFRACTION100
2.9714-3.74310.20661470.16562729X-RAY DIFFRACTION100
3.7431-90.22631670.18442819X-RAY DIFFRACTION99
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)
13.17990.82722.05611.22641.27081.9288-0.1377-0.16690.1206-0.0303-0.04530.1037-0.1514-0.10970.16550.12050.00180.00970.12290.00690.0957-14.7939-6.499619.1863
25.52622.3381-1.37379.8553-4.69686.3865-0.14680.74680.5823-0.13530.2025-0.5298-0.50290.4196-0.00730.1659-0.0402-0.01330.25790.02190.22111.91243.08120.3688
36.0291-3.6983-4.62183.23052.87453.7071-0.00850.0360.5089-0.45230.0731-0.5799-0.97140.6139-0.14720.4551-0.141-0.09260.36770.15360.4116-3.932510.46619.2075
41.54610.49132.32530.69592.17447.2481-0.3459-0.04290.4068-0.2911-0.03410.0329-0.9063-0.63890.37150.29280.0483-0.05880.19880.01390.1876-12.90325.792522.7783
52.1201-0.5547-0.81212.40050.85172.3562-0.02060.17340.2474-0.21110.0453-0.1307-0.0765-0.0639-0.01870.1750.02660.01230.2110.03670.1667-12.4364-8.24924.456
67.5654-1.93611.23511.17151.15653.4148-0.1703-0.07080.6577-0.880.1659-0.6262-0.7816-0.178-0.15770.50720.00780.13080.22980.11690.4338-6.33765.98334.0255
77.20662.3783-2.88485.0293-2.41731.92750.06750.01380.3305-0.04560.0363-0.3486-0.58970.9735-0.05210.2819-0.08520.00350.3106-0.06210.21580.8975-2.681411.6053
85.23041.3223-0.58016.6201-3.27996.8016-0.0574-0.4224-0.31580.52740.1299-0.35750.04030.1841-0.05190.15820.0441-0.06530.1755-0.00130.1563-6.3404-11.878121.7601
96.11342.5371-3.74254.9069-2.99647.45460.0613-0.0904-0.19680.1602-0.0411-0.12410.06320.2690.0450.09310.0269-0.00920.1401-0.01480.1353-7.6789-15.794214.4283
105.3023-2.5951.02663.22162.00236.50290.00360.11030.4217-0.116-0.0243-0.4439-0.92151.1887-0.02370.2648-0.07710.07530.38540.05230.24940.853-4.71851.7504
113.5673-0.8238-0.72072.58211.01131.6134-0.0286-0.16620.24550.07680.0496-0.09810.00760.05350.00140.108-0.0072-0.00220.11580.00560.1206-31.12211.920210.3085
126.7426-0.78444.1546.12750.83743.71180.0009-0.3743-1.09840.70070.30170.47750.5353-1.027-0.2940.28350.01820.02220.29510.00940.331-41.87193.679224.5581
137.4841-5.2630.88596.9278-1.41313.8576-0.2908-1.02730.330.84110.8713-1.7188-0.15950.5794-0.34520.33720.0536-0.13120.3446-0.1950.5426-31.955311.146523.7235
142.27811.81831.38866.01314.58067.113-0.2599-0.56590.37610.90410.1882-0.00180.1929-0.1930.08470.26480.0794-0.0080.2343-0.05620.1778-29.7745-0.526420.1291
156.87283.19045.35486.50535.28776.72020.3145-0.2619-0.56970.18450.1291-0.40610.32730.067-0.38380.13160.0097-0.00110.15660.01310.1645-31.43-12.00266.7543
165.44241.1150.79546.71510.93180.20770.5126-1.3387-0.13712.2087-0.46330.73311.2318-0.7218-0.0410.8057-0.3439-0.01450.77310.14970.5186-37.795-15.766616.4711
173.9293-1.85794.01412.8078-1.15934.3754-0.3984-1.2441-0.26690.66930.27430.13630.6068-0.67630.09590.7332-0.10840.36251.01890.04420.6549-42.1184-9.712921.8246
188.65763.9257-4.0979.0781-3.72117.10950.08390.3670.26480.0287-0.05530.57110.1028-0.6531-0.03970.13290.02410.00140.1991-0.07290.1738-40.16491.12587.2107
194.32715.2427-3.02596.6627-3.40284.3999-0.11410.45690.151-0.06990.06760.48130.0828-0.6115-0.00410.14330.00540.03240.1832-0.05820.2067-36.9681-3.43210.3935
201.62191.696-0.36512.1547-0.88360.74120.1643-0.15790.02220.4318-0.06470.45740.0669-0.12810.20590.8692-0.40540.4660.1891-0.16090.8999-46.3671-14.39711.5131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:26)
2X-RAY DIFFRACTION2(chain A and resid 27:33)
3X-RAY DIFFRACTION3(chain A and resid 34:37)
4X-RAY DIFFRACTION4(chain A and resid 38:60)
5X-RAY DIFFRACTION5(chain A and resid 61:83)
6X-RAY DIFFRACTION6(chain A and resid 84:90)
7X-RAY DIFFRACTION7(chain A and resid 91:99)
8X-RAY DIFFRACTION8(chain A and resid 100:111)
9X-RAY DIFFRACTION9(chain A and resid 112:128)
10X-RAY DIFFRACTION10(chain A and resid 129:137)
11X-RAY DIFFRACTION11(chain B and resid 1:30)
12X-RAY DIFFRACTION12(chain B and resid 31:39)
13X-RAY DIFFRACTION13(chain B and resid 40:50)
14X-RAY DIFFRACTION14(chain B and resid 51:60)
15X-RAY DIFFRACTION15(chain B and resid 61:77)
16X-RAY DIFFRACTION16(chain B and resid 78:86)
17X-RAY DIFFRACTION17(chain B and resid 87:94)
18X-RAY DIFFRACTION18(chain B and resid 95:111)
19X-RAY DIFFRACTION19(chain B and resid 112:128)
20X-RAY DIFFRACTION20(chain B and resid 129:137)

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