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- PDB-7sji: Crystal structure of dehaloperoxidase B in complex with R-(+)-limonene -

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Basic information

Entry
Database: PDB / ID: 7sji
TitleCrystal structure of dehaloperoxidase B in complex with R-(+)-limonene
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
(4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / 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: 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
Water1,74797
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5437
Polymers15,4141
Non-polymers1,1296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2594
Polymers15,4141
Non-polymers8453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.775, 66.988, 67.759
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 (bacteria) / Variant (production host): Gold(DE3) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 106 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-9IR / (4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene / R-(+)-limonene


Mass: 136.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
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: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→33.9 Å / Num. obs: 27041 / % possible obs: 97.88 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 27.6
Reflection shellResolution: 1.76→1.806 Å / Num. unique obs: 1860 / CC1/2: 0.784

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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: 1.76→33.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.028 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2323 1255 4.641 %
Rwork0.1946 25786 -
all0.196 --
obs-27041 97.882 %
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: 35.759 Å2
Baniso -1Baniso -2Baniso -3
1-1.776 Å20 Å20 Å2
2---0.601 Å20 Å2
3----1.175 Å2
Refinement stepCycle: LAST / Resolution: 1.76→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 134 97 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132761
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152486
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.6963814
X-RAY DIFFRACTIONr_angle_other_deg1.5471.6385756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27822.876153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07715471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9451518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2334
X-RAY DIFFRACTIONr_chiral_restr_other0.0450.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023444
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02724
X-RAY DIFFRACTIONr_nbd_refined0.2710.2782
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22465
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2135
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0750.217
X-RAY DIFFRACTIONr_nbd_other0.1720.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.218
X-RAY DIFFRACTIONr_mcbond_it2.0573.1271310
X-RAY DIFFRACTIONr_mcbond_other2.0563.1331311
X-RAY DIFFRACTIONr_mcangle_it2.9124.6921693
X-RAY DIFFRACTIONr_mcangle_other2.9134.6941694
X-RAY DIFFRACTIONr_scbond_it2.7313.5061451
X-RAY DIFFRACTIONr_scbond_other2.7193.51444
X-RAY DIFFRACTIONr_scangle_it4.0345.1732098
X-RAY DIFFRACTIONr_scangle_other4.0255.1652087
X-RAY DIFFRACTIONr_lrange_it7.70538.8133447
X-RAY DIFFRACTIONr_lrange_other7.70138.7443436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8060.311840.2741860X-RAY DIFFRACTION97.2486
1.806-1.8550.322860.2341834X-RAY DIFFRACTION98.5626
1.855-1.9090.2551020.2291784X-RAY DIFFRACTION98.6402
1.909-1.9670.259840.2321741X-RAY DIFFRACTION98.7554
1.967-2.0320.253690.2281694X-RAY DIFFRACTION98.3817
2.032-2.1030.273980.21618X-RAY DIFFRACTION98.6207
2.103-2.1820.278780.1941596X-RAY DIFFRACTION98.7028
2.182-2.2710.233730.1951506X-RAY DIFFRACTION98.2576
2.271-2.3720.206780.1781471X-RAY DIFFRACTION98.7253
2.372-2.4870.247640.1791392X-RAY DIFFRACTION97.5871
2.487-2.6210.249610.1971343X-RAY DIFFRACTION98.2505
2.621-2.780.231570.1881258X-RAY DIFFRACTION97.6244
2.78-2.9710.263460.1961202X-RAY DIFFRACTION97.729
2.971-3.2080.262540.21119X-RAY DIFFRACTION97.9132
3.208-3.5130.243490.1881012X-RAY DIFFRACTION95.8446
3.513-3.9250.215410.184937X-RAY DIFFRACTION97.1202
3.925-4.5270.163620.175782X-RAY DIFFRACTION94.725
4.527-5.5320.216380.178701X-RAY DIFFRACTION97.1091
5.532-7.7710.261210.211590X-RAY DIFFRACTION99.3496
7.771-33.90.36100.211336X-RAY DIFFRACTION90.8137
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)
10.3548-0.4609-0.17341.8446-0.66790.7256-0.05-0.0014-0.01630.2051-0.051-0.1089-0.08050.0410.1010.0482-0.021-0.01270.01340.00620.01445.62832.2437-21.3287
20.41080.1868-0.30210.44-0.57981.4154-0.052-0.04210.0204-0.11340.06250.02560.1538-0.0648-0.01050.0642-0.01350.00670.02310.00250.0077-21.32474.9138-19.2049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

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