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- PDB-7t9e: Crystal structure of dehaloperoxidase B in complex with +(-)-limo... -

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Basic information

Entry
Database: PDB / ID: 7t9e
TitleCrystal structure of dehaloperoxidase B in complex with +(-)-limonene oxide
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Chem-GH9 / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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

Downloads & links

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Assembly

Deposited unit
AAA: Dehaloperoxidase B
BBB: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,83911
Polymers30,8292
Non-polymers2,0109
Water2,360131
1
AAA: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4676
Polymers15,4141
Non-polymers1,0535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3715
Polymers15,4141
Non-polymers9574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.996, 66.742, 67.859
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 AAABBB

#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, 140 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-GH9 / (1R,4R,6S)-1-methyl-4-(prop-1-en-2-yl)-7-oxabicyclo[4.1.0]heptane / +(-)-limonene oxide


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / 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: 1.57→36.81 Å / Num. obs: 35061 / % possible obs: 93.5 % / Redundancy: 4 % / CC1/2: 0.999 / Net I/σ(I): 22.67
Reflection shellResolution: 1.57→1.611 Å / Num. unique obs: 2582 / CC1/2: 0.66

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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: 1.57→36.81 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.198 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2181 1668 4.757 %
Rwork0.1432 33393 -
all0.147 --
obs-35061 93.511 %
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: 26.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.626 Å2-0 Å2-0 Å2
2---2.316 Å20 Å2
3---2.942 Å2
Refinement stepCycle: LAST / Resolution: 1.57→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 135 131 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132810
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152564
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.6943886
X-RAY DIFFRACTIONr_angle_other_deg1.5721.6445961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57923.113151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50715502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3651517
X-RAY DIFFRACTIONr_chiral_restr0.1150.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023456
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02718
X-RAY DIFFRACTIONr_nbd_refined0.2650.2834
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22329
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21324
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21030
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2137
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.228
X-RAY DIFFRACTIONr_nbd_other0.2420.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it4.2792.4511327
X-RAY DIFFRACTIONr_mcbond_other4.2482.4471326
X-RAY DIFFRACTIONr_mcangle_it4.8283.7051719
X-RAY DIFFRACTIONr_mcangle_other4.833.7081720
X-RAY DIFFRACTIONr_scbond_it5.6582.9061483
X-RAY DIFFRACTIONr_scbond_other5.4742.9011472
X-RAY DIFFRACTIONr_scangle_it6.3794.1922137
X-RAY DIFFRACTIONr_scangle_other6.334.1832120
X-RAY DIFFRACTIONr_lrange_it6.64431.3033544
X-RAY DIFFRACTIONr_lrange_other6.5931.1753527
X-RAY DIFFRACTIONr_rigid_bond_restr4.78835374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.6110.2991400.2532582X-RAY DIFFRACTION99.1621
1.611-1.6550.271140.2172521X-RAY DIFFRACTION98.9486
1.655-1.7030.281200.1892432X-RAY DIFFRACTION98.5328
1.703-1.7550.2361100.1682345X-RAY DIFFRACTION98.2
1.755-1.8130.2111040.1392281X-RAY DIFFRACTION97.5859
1.813-1.8760.2011250.1182150X-RAY DIFFRACTION96.4801
1.876-1.9470.2441050.1082074X-RAY DIFFRACTION94.4517
1.947-2.0260.1891020.0961902X-RAY DIFFRACTION90.6787
2.026-2.1160.1981000.1161862X-RAY DIFFRACTION93.6069
2.116-2.2190.235840.1261810X-RAY DIFFRACTION93.3465
2.219-2.3390.186850.121731X-RAY DIFFRACTION94.0445
2.339-2.480.195860.1091621X-RAY DIFFRACTION92.9739
2.48-2.6510.225860.1171543X-RAY DIFFRACTION94.3254
2.651-2.8630.213520.1261431X-RAY DIFFRACTION92.2838
2.863-3.1350.262620.1381268X-RAY DIFFRACTION88.9037
3.135-3.5030.207570.1461063X-RAY DIFFRACTION81.8713
3.503-4.0410.188390.13811X-RAY DIFFRACTION70.2479
4.041-4.9410.169400.146823X-RAY DIFFRACTION83.0606
4.941-6.950.224330.206712X-RAY DIFFRACTION90.0846
6.95-36.810.307240.241422X-RAY DIFFRACTION88.8446

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