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- PDB-7sjc: Crystal structure of dehaloperoxidase B in complex with gamma-ter... -

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Basic information

Entry
Database: PDB / ID: 7sjc
TitleCrystal structure of dehaloperoxidase B in complex with gamma-terpinene
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-yl)cyclohexa-1,4-diene / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMalewschik, T. / Yun, D. / de Serrano, V.S. / Ghiladi, R.A.
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 18, 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
Water2,252125
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
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
Unit cell
Length a, b, c (Å)59.817, 67.606, 67.620
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, 134 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-9NI / 1-methyl-4-(propan-2-yl)cyclohexa-1,4-diene


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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
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→47.81 Å / Num. obs: 30764 / % possible obs: 99.81 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 9.1 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 2118 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.7→47.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.204 / SU B: 3.864 / SU ML: 0.12 / Average fsc free: 0.8536 / Average fsc work: 0.8674 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2453 1408 4.577 %
Rwork0.1989 29356 -
all0.201 --
obs-30764 99.805 %
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: 30.962 Å2
Baniso -1Baniso -2Baniso -3
1-4.039 Å20 Å2-0 Å2
2---2.575 Å20 Å2
3----1.464 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 134 125 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132738
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152491
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.73775
X-RAY DIFFRACTIONr_angle_other_deg1.4241.6425783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51423.265147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68515482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4731516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023391
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02697
X-RAY DIFFRACTIONr_nbd_refined0.2610.2783
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.22429
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21322
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.212
X-RAY DIFFRACTIONr_nbd_other0.2080.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.224
X-RAY DIFFRACTIONr_mcbond_it2.2053.1191296
X-RAY DIFFRACTIONr_mcbond_other2.2053.1231297
X-RAY DIFFRACTIONr_mcangle_it3.1844.6731673
X-RAY DIFFRACTIONr_mcangle_other3.1844.6761674
X-RAY DIFFRACTIONr_scbond_it2.8783.3941442
X-RAY DIFFRACTIONr_scbond_other2.8643.3941435
X-RAY DIFFRACTIONr_scangle_it4.3024.9952079
X-RAY DIFFRACTIONr_scangle_other4.2864.9942068
X-RAY DIFFRACTIONr_lrange_it7.88638.2553441
X-RAY DIFFRACTIONr_lrange_other7.88338.2013422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.356980.33221180.33322180.5810.58299.90980.313
1.744-1.7920.3141020.30820910.30821940.6850.68199.95440.286
1.792-1.8440.31980.27120410.27321410.7850.77399.90660.246
1.844-1.90.304990.25319440.25520430.8070.8211000.229
1.9-1.9630.271890.23119480.23320380.8730.85899.95090.207
1.963-2.0310.306890.2118260.21319160.8440.90699.94780.191
2.031-2.1080.201940.19517880.19518840.9260.91999.89380.181
2.108-2.1940.223780.18917230.19118040.9010.92699.83370.177
2.194-2.2910.283860.19416700.19817610.8830.9399.71610.184
2.291-2.4030.26740.18315920.18616700.9110.9499.76050.177
2.403-2.5320.254770.17914810.18315590.9240.94499.93590.178
2.532-2.6850.25650.19114620.19415280.9160.93699.93460.192
2.685-2.870.225500.19513550.19614130.9130.92599.43380.199
2.87-3.0990.274650.19212690.19613440.9140.93799.2560.203
3.099-3.3940.252550.19811690.212260.9190.94199.83690.212
3.394-3.7920.206460.18410820.18411330.9430.95799.55870.203
3.792-4.3740.2690.1729210.1749950.9530.96399.49750.195
4.374-5.3460.213380.188170.1818560.9470.95999.88320.211
5.346-7.5130.209200.2026670.2026890.9520.95199.70970.232
7.513-47.810.344160.2073920.2124120.90.94899.02910.268

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