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- PDB-7sjd: Crystal structure of dehaloperoxidase B in complex with terpinolene -

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Basic information

Entry
Database: PDB / ID: 7sjd
TitleCrystal structure of dehaloperoxidase B in complex with terpinolene
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
1-methyl-4-(propan-2-ylidene)cyclohex-1-ene / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Yun, D. / Malewschik, T.
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: Malewschick, T. / Yun, D. / de Serrano, V. / Ghiladi, R.A.
History
DepositionOct 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,80311
Polymers30,8292
Non-polymers1,9749
Water2,000111
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4516
Polymers15,4141
Non-polymers1,0375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3515
Polymers15,4141
Non-polymers9374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.711, 67.574, 67.856
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-9LR / 1-methyl-4-(propan-2-ylidene)cyclohex-1-ene


Mass: 136.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16 / 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.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsLIGAND 9LR OCCUPIES DENSITY THAT IS CLOSE TO THE POSITION OF H55 IN ITS ALTERNATE CONFORMATION. THE ...LIGAND 9LR 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.383 Å / Num. obs: 30227 / % possible obs: 98.52 % / Redundancy: 4.6 % / CC1/2: 0.996 / Net I/σ(I): 30.3
Reflection shellResolution: 1.703→1.748 Å / Num. unique obs: 1853 / CC1/2: 0.547

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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: 1.703→37.383 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.479 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2247 1383 4.575 %
Rwork0.1859 28844 -
all0.188 --
obs-30227 98.517 %
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: 31.851 Å2
Baniso -1Baniso -2Baniso -3
1-1.603 Å20 Å20 Å2
2---0.669 Å20 Å2
3----0.934 Å2
Refinement stepCycle: LAST / Resolution: 1.703→37.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 134 111 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132738
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152467
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.6993781
X-RAY DIFFRACTIONr_angle_other_deg1.5321.645729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2423.224152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0551517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023421
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02705
X-RAY DIFFRACTIONr_nbd_refined0.2840.2749
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.22401
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21327
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2114
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0990.223
X-RAY DIFFRACTIONr_nbd_other0.2030.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.216
X-RAY DIFFRACTIONr_mcbond_it1.6022.6571297
X-RAY DIFFRACTIONr_mcbond_other1.6022.6611298
X-RAY DIFFRACTIONr_mcangle_it2.3753.9841676
X-RAY DIFFRACTIONr_mcangle_other2.3763.9861677
X-RAY DIFFRACTIONr_scbond_it2.2472.9961441
X-RAY DIFFRACTIONr_scbond_other2.2422.9931434
X-RAY DIFFRACTIONr_scangle_it3.4424.4042082
X-RAY DIFFRACTIONr_scangle_other3.4384.3982071
X-RAY DIFFRACTIONr_lrange_it6.96433.1483391
X-RAY DIFFRACTIONr_lrange_other6.90433.0493375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.703-1.7480.31870.3131853X-RAY DIFFRACTION88.1818
1.748-1.7950.314930.2671980X-RAY DIFFRACTION95.8834
1.795-1.8470.2861020.2462017X-RAY DIFFRACTION98.3295
1.847-1.9040.274930.231912X-RAY DIFFRACTION99.1102
1.904-1.9660.274900.221935X-RAY DIFFRACTION99.9013
1.966-2.0350.249900.1941825X-RAY DIFFRACTION100
2.035-2.1120.205910.1871801X-RAY DIFFRACTION99.9472
2.112-2.1980.218810.1751717X-RAY DIFFRACTION100
2.198-2.2960.239830.1711643X-RAY DIFFRACTION99.8843
2.296-2.4070.261760.1691588X-RAY DIFFRACTION99.88
2.407-2.5370.232760.1641485X-RAY DIFFRACTION99.7444
2.537-2.6910.244620.1861447X-RAY DIFFRACTION99.8016
2.691-2.8760.245480.1851352X-RAY DIFFRACTION99.5733
2.876-3.1050.22660.181261X-RAY DIFFRACTION99.4007
3.105-3.40.211550.1831174X-RAY DIFFRACTION99.7565
3.4-3.7990.235450.1781063X-RAY DIFFRACTION99.73
3.799-4.3820.192710.165919X-RAY DIFFRACTION99.8991
4.382-5.3560.193380.175821X-RAY DIFFRACTION99.8837
5.356-7.5280.114200.186666X-RAY DIFFRACTION100
7.528-37.3830.305160.206385X-RAY DIFFRACTION98.044
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)
10.31520.54070.07351.7473-0.4050.3617-0.0591-0.0006-0.0194-0.19940.0135-0.11170.0554-0.00730.04550.09460.01750.00880.0064-0.00560.01845.6047-2.156521.2696
20.6257-0.03840.24430.4256-0.59031.0996-0.01510.0316-0.03620.08740.0230.0016-0.1225-0.0683-0.00790.10010.01570.00090.01830.00040.0052-21.4156-5.09419.3214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

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