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- PDB-7t9c: Crystal structure of dehaloperoxidase B in complex with thymol -

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Basic information

Entry
Database: PDB / ID: 7t9c
TitleCrystal structure of dehaloperoxidase B in complex with thymol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / dehaloperoxidase B / heme peroxidase / peroxigenase / oxygen binding / heme cofactor
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 domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
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: 1.73 Å
Authorsde Serrano, V.S. / Ghiladi, R.A. / 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: Malewschik, T. / de Serrano, V.S. / Yun, D. / Ghiladi, R.A.
History
DepositionDec 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,19915
Polymers30,8292
Non-polymers2,37013
Water1,928107
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,83410
Polymers15,4141
Non-polymers1,4199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3655
Polymers15,4141
Non-polymers9514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.451, 66.792, 67.951
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(DE3) (bacteria) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 120 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPB / 5-METHYL-2-(1-METHYLETHYL)PHENOL


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


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.: 107 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion / 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-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→29.99 Å / Num. obs: 27496 / % possible obs: 96.7 % / Redundancy: 4 % / CC1/2: 0.995 / Net I/σ(I): 20.5
Reflection shellResolution: 1.73→1.789 Å / Num. unique obs: 1983 / CC1/2: 0.712

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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: 1.73→29.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.161 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2068 1271 4.622 %
Rwork0.1826 26225 -
all0.184 --
obs-27496 96.694 %
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: 25.796 Å2
Baniso -1Baniso -2Baniso -3
1-1.553 Å20 Å20 Å2
2---0.493 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 160 107 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132758
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152498
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.6963795
X-RAY DIFFRACTIONr_angle_other_deg1.5681.6395788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12723.289149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13915471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2911516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023444
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02704
X-RAY DIFFRACTIONr_nbd_refined0.2550.2782
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22408
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21309
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.222
X-RAY DIFFRACTIONr_nbd_other0.2360.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.223
X-RAY DIFFRACTIONr_mcbond_it1.6492.1141295
X-RAY DIFFRACTIONr_mcbond_other1.6482.1171296
X-RAY DIFFRACTIONr_mcangle_it2.5943.1641670
X-RAY DIFFRACTIONr_mcangle_other2.5953.1671671
X-RAY DIFFRACTIONr_scbond_it2.3772.4961463
X-RAY DIFFRACTIONr_scbond_other2.3712.4931456
X-RAY DIFFRACTIONr_scangle_it3.5963.6632104
X-RAY DIFFRACTIONr_scangle_other3.5883.6562093
X-RAY DIFFRACTIONr_lrange_it6.35926.863400
X-RAY DIFFRACTIONr_lrange_other6.35326.7933390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.7750.253830.2711983X-RAY DIFFRACTION99.6143
1.775-1.8230.278980.2381904X-RAY DIFFRACTION99.3056
1.823-1.8760.264940.2141831X-RAY DIFFRACTION98.8701
1.876-1.9340.269870.261771X-RAY DIFFRACTION96.8213
1.934-1.9970.232820.2121684X-RAY DIFFRACTION95.4079
1.997-2.0670.219800.1941615X-RAY DIFFRACTION95.1178
2.067-2.1450.239730.1861650X-RAY DIFFRACTION99.023
2.145-2.2320.241790.1771550X-RAY DIFFRACTION97.8966
2.232-2.3310.234830.1951477X-RAY DIFFRACTION97.0753
2.331-2.4450.25690.1591452X-RAY DIFFRACTION99.282
2.445-2.5770.185680.1491392X-RAY DIFFRACTION99.5907
2.577-2.7330.169570.1651315X-RAY DIFFRACTION98.7761
2.733-2.9210.232440.1641249X-RAY DIFFRACTION98.7023
2.921-3.1540.214630.1751125X-RAY DIFFRACTION97.0588
3.154-3.4530.245460.171970X-RAY DIFFRACTION88.8112
3.453-3.8580.161370.154790X-RAY DIFFRACTION79.4428
3.858-4.450.144600.154795X-RAY DIFFRACTION92.4324
4.45-5.4390.16360.174708X-RAY DIFFRACTION96
5.439-7.6420.228230.227601X-RAY DIFFRACTION97.8056
7.642-29.990.25190.201359X-RAY DIFFRACTION94.8454
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)
10.20560.23660.21071.4685-0.19950.3862-0.01340.0042-0.001-0.10890.0084-0.04860.02980.01090.0050.020.014-0.00280.019-0.00450.02595.7044-2.211821.1175
20.278-0.45340.34521.1934-0.95341.2698-0.06870.013-0.02420.14920.0980.0054-0.1352-0.0963-0.02930.02440.00570.00140.04140.00070.0183-21.0347-4.495619.2068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

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