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- PDB-7t9d: Crystal structure of dehaloperoxidase B in complex with -(-) limo... -

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Basic information

Entry
Database: PDB / ID: 7t9d
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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-GHI / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
Authorsde Serran, 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. / 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
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26715
Polymers30,8292
Non-polymers2,43813
Water2,432135
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6528
Polymers15,4141
Non-polymers1,2377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6167
Polymers15,4141
Non-polymers1,2016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.657, 66.492, 68.340
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, 148 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GHI / (1S,4S,6R)-1-methyl-4-(prop-1-en-2-yl)-7-oxabicyclo[4.1.0]heptane / -(-) limonene oxide


Mass: 152.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16O / Feature type: SUBJECT OF INVESTIGATION
#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.: 135 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
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: 1.66→34.193 Å / Num. obs: 31407 / % possible obs: 97.3 % / Redundancy: 3.7 % / CC1/2: 0.975 / Net I/σ(I): 15.3
Reflection shellResolution: 1.66→1.703 Å / Num. unique obs: 2247 / CC1/2: 0.447

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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: 1.66→34.193 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.701 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2341 1602 5.101 %
Rwork0.1659 29805 -
all0.169 --
obs-31407 97.314 %
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: 24.037 Å2
Baniso -1Baniso -2Baniso -3
1--1.979 Å2-0 Å2-0 Å2
2---1.295 Å20 Å2
3---3.274 Å2
Refinement stepCycle: LAST / Resolution: 1.66→34.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 164 135 2431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132782
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152510
X-RAY DIFFRACTIONr_angle_refined_deg1.831.6923845
X-RAY DIFFRACTIONr_angle_other_deg1.5681.655822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89723.113151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8661517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023409
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02713
X-RAY DIFFRACTIONr_nbd_refined0.270.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2290.22436
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21307
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2980.222
X-RAY DIFFRACTIONr_nbd_other0.2750.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.214
X-RAY DIFFRACTIONr_mcbond_it3.4991.8671305
X-RAY DIFFRACTIONr_mcbond_other3.4311.8651304
X-RAY DIFFRACTIONr_mcangle_it4.2072.8191687
X-RAY DIFFRACTIONr_mcangle_other4.2132.8211688
X-RAY DIFFRACTIONr_scbond_it5.7882.4811477
X-RAY DIFFRACTIONr_scbond_other5.5922.4611466
X-RAY DIFFRACTIONr_scangle_it7.0933.5862128
X-RAY DIFFRACTIONr_scangle_other6.7413.5562111
X-RAY DIFFRACTIONr_lrange_it7.07725.5453468
X-RAY DIFFRACTIONr_lrange_other7.03125.3473446
X-RAY DIFFRACTIONr_rigid_bond_restr11.79135292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.7030.3111100.2312247X-RAY DIFFRACTION99.6196
1.703-1.750.2651070.2022173X-RAY DIFFRACTION99.6503
1.75-1.80.2731020.1912116X-RAY DIFFRACTION99.6406
1.8-1.8560.2621010.1682038X-RAY DIFFRACTION99.581
1.856-1.9160.2641290.1531973X-RAY DIFFRACTION99.6209
1.916-1.9840.2531060.1471883X-RAY DIFFRACTION98.4653
1.984-2.0580.2521030.1481775X-RAY DIFFRACTION95.6212
2.058-2.1420.2411000.1511809X-RAY DIFFRACTION99.5827
2.142-2.2370.188920.1341707X-RAY DIFFRACTION99.5573
2.237-2.3460.204960.1361647X-RAY DIFFRACTION99.3729
2.346-2.4730.213760.1321559X-RAY DIFFRACTION98.6723
2.473-2.6220.226900.1341451X-RAY DIFFRACTION97.7792
2.622-2.8030.213710.1441376X-RAY DIFFRACTION96.5955
2.803-3.0260.247520.1471282X-RAY DIFFRACTION95.8333
3.026-3.3140.228700.1671141X-RAY DIFFRACTION94.4618
3.314-3.7030.239560.17979X-RAY DIFFRACTION87.7863
3.703-4.2710.21430.164885X-RAY DIFFRACTION89.4027
4.271-5.2210.217440.184755X-RAY DIFFRACTION88.9755
5.221-7.340.251330.23636X-RAY DIFFRACTION93.1755
7.34-34.1930.276210.265369X-RAY DIFFRACTION90.2778
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)
10.01980.0125-0.00220.0491-0.04570.048-0.00230.00290.002-0.00440.00240.00110.0010.0008-0.00020.0702-0.0001-0.00050.044-0.00030.00085.872-2.409921.3795
20.02970.00310.0140.0156-0.02250.0482-0.00270.00260.00040.0049-0.0013-0.0022-0.0067-0.00410.00390.06930.0002-0.00010.04210.00050.0004-21.1499-4.659519.3045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

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