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- PDB-8vqs: Crystal structure of Dehaloperoxidase B in complex with substrate... -

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Basic information

Entry
Database: PDB / ID: 8vqs
TitleCrystal structure of Dehaloperoxidase B in complex with substrate cyclohexene
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / peroxidase / peroxigenase / oxidase / oxigenase / globin / heme cofactor / oxygen binding / hydrogen peroxide cofactor / halophenol binding / substrates
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
: / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsde Serrano, V.S. / Yun, D. / Ghiladi, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Structure of Dehaloperoxidase B in complex with cyclohexene
Authors: Yun, D. / de Serrano, V.S. / Ghiladi, R.A.
History
DepositionJan 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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)33,14916
Polymers30,8292
Non-polymers2,32014
Water1,964109
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,84811
Polymers15,4141
Non-polymers1,43310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3015
Polymers15,4141
Non-polymers8874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.092, 67.684, 67.684
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 , 6 types, 123 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-A1ADK / cyclohexene


Mass: 82.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 43.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPEG 2000, ammonium sulfate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→17.34 Å / Num. obs: 18829 / % possible obs: 99.47 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 16
Reflection shellResolution: 2→2.051 Å / Num. unique obs: 1241 / CC1/2: 0.705

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→17.339 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.125 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.262 / ESU R Free: 0.204
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.251 929 4.934 %
Rwork0.1946 17900 -
all0.198 --
obs-18829 99.466 %
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: 38.438 Å2
Baniso -1Baniso -2Baniso -3
1-1.496 Å2-0 Å20 Å2
2---1.135 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→17.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 152 109 2423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122833
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162611
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.7023889
X-RAY DIFFRACTIONr_angle_other_deg0.5491.6296067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.995519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29610516
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.56910138
X-RAY DIFFRACTIONr_chiral_restr0.070.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023549
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02727
X-RAY DIFFRACTIONr_nbd_refined0.2680.2808
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.22433
X-RAY DIFFRACTIONr_nbtor_refined0.1990.21336
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.220
X-RAY DIFFRACTIONr_nbd_other0.1770.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.216
X-RAY DIFFRACTIONr_mcbond_it3.2843.7571319
X-RAY DIFFRACTIONr_mcbond_other3.2843.7571319
X-RAY DIFFRACTIONr_mcangle_it4.6246.761705
X-RAY DIFFRACTIONr_mcangle_other4.6236.7621706
X-RAY DIFFRACTIONr_scbond_it4.4344.161514
X-RAY DIFFRACTIONr_scbond_other4.4114.1471499
X-RAY DIFFRACTIONr_scangle_it6.4227.5032163
X-RAY DIFFRACTIONr_scangle_other6.4147.4842140
X-RAY DIFFRACTIONr_lrange_it8.54939.9383555
X-RAY DIFFRACTIONr_lrange_other8.52539.6523538
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
2-2.0510.435710.42512410.42613750.9240.93895.41820.385
2.051-2.1070.454600.32312410.32813010.9160.9541000.283
2.107-2.1670.277480.27312380.27312860.9480.9631000.235
2.167-2.2320.267670.2411840.24212510.9490.9671000.202
2.232-2.3040.323740.21411540.22112280.9350.971000.179
2.304-2.3840.282600.18711030.19211630.9550.9761000.155
2.384-2.4720.248580.17510980.17811560.9630.9791000.148
2.472-2.5710.214430.17510690.17711120.9660.981000.147
2.571-2.6820.253370.17510110.17810480.9620.981000.15
2.682-2.810.233560.1889700.1910260.9650.9781000.167
2.81-2.9580.236560.1829150.1859710.9630.9831000.166
2.958-3.1310.225400.1898650.199050.970.9821000.172
3.131-3.340.213320.218350.218670.9740.9771000.197
3.34-3.5960.256470.1997820.2028290.9580.9811000.193
3.596-3.9230.26390.1867180.197570.9580.9821000.181
3.923-4.3580.188500.1486400.1516900.980.9871000.149
4.358-4.980.217270.1396040.1416310.9770.9881000.142
4.98-5.9770.252330.1945130.1975460.9720.9851000.196
5.977-7.9910.177140.2094280.2084420.9710.9841000.212
7.991-17.3390.397170.2332910.2423080.9690.9821000.248

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