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- PDB-8vzr: Crystal structure of dehaloperoxidase A in complex with substrate... -

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Basic information

Entry
Database: PDB / ID: 8vzr
TitleCrystal structure of dehaloperoxidase A in complex with substrate 4-bromo-o-cresol
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidsase / peroxygenase / oxidase / oxygenase / globin / heme cofactor / oxygen binding / hydrogen preoxide cosubstrate / halophenol binding / substrate
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 / 4-bromo-2-methylphenol / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsAktar, M.S. / de Serrano, V.S. / Ghiladi, R.A. / Franzen, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2024
Title: Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B.
Authors: Aktar, M.S. / de Serrano, V. / Ghiladi, R.A. / Franzen, S.
History
DepositionFeb 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehaloperoxidase A
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,82718
Polymers31,0972
Non-polymers2,73016
Water3,243180
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8738
Polymers15,5491
Non-polymers1,3247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,95510
Polymers15,5491
Non-polymers1,4069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.404, 67.756, 68.169
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 A


Mass: 15548.597 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: Q9NAV8

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Non-polymers , 8 types, 196 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-MWJ / 4-bromo-2-methylphenol


Mass: 187.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7BrO
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPEG2000, ammonium sulfate, sodium 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: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→37.14 Å / Num. obs: 33787 / % possible obs: 99.79 % / Redundancy: 9.3 % / CC1/2: 0.987 / Net I/σ(I): 30.8
Reflection shellResolution: 1.64→1.682 Å / Num. unique obs: 2361 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFK

2qfk


Resolution: 1.64→37.136 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.841 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2044 1678 4.966 %
Rwork0.1559 32109 -
all0.158 --
obs-33787 99.787 %
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: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.435 Å2-0 Å20 Å2
2---0.47 Å2-0 Å2
3---0.035 Å2
Refinement stepCycle: LAST / Resolution: 1.64→37.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 175 180 2535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122866
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162606
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.7093907
X-RAY DIFFRACTIONr_angle_other_deg0.6141.6196031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3585358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.581518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33610499
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.75310140
X-RAY DIFFRACTIONr_chiral_restr0.0860.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023546
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02746
X-RAY DIFFRACTIONr_nbd_refined0.3250.2828
X-RAY DIFFRACTIONr_symmetry_nbd_other0.240.22318
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21360
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21311
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3250.256
X-RAY DIFFRACTIONr_nbd_other0.3390.2197
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.228
X-RAY DIFFRACTIONr_mcbond_it0.961.7411311
X-RAY DIFFRACTIONr_mcbond_other0.9581.7411311
X-RAY DIFFRACTIONr_mcangle_it1.1963.1311692
X-RAY DIFFRACTIONr_mcangle_other1.1963.1321693
X-RAY DIFFRACTIONr_scbond_it1.0952.1311555
X-RAY DIFFRACTIONr_scbond_other1.0922.1351546
X-RAY DIFFRACTIONr_scangle_it1.3843.7512207
X-RAY DIFFRACTIONr_scangle_other1.3823.7542196
X-RAY DIFFRACTIONr_lrange_it2.05827.6363706
X-RAY DIFFRACTIONr_lrange_other2.03427.1693678
X-RAY DIFFRACTIONr_rigid_bond_restr3.84535472
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
1.64-1.6820.3211120.28623610.28724760.9420.95999.87880.269
1.682-1.7280.3131200.2322860.23424060.9440.9691000.197
1.728-1.7780.224860.17522400.17723270.9670.98199.9570.14
1.778-1.8330.2241230.14421530.14822760.9690.9861000.116
1.833-1.8930.2181200.12620720.13121920.9720.9891000.1
1.893-1.9590.1711320.12920110.13221430.9790.9891000.106
1.959-2.0330.1841030.12919460.13220490.9810.9891000.109
2.033-2.1160.1911030.12618880.1319910.9780.991000.109
2.116-2.210.1791130.13117950.13419080.9810.991000.117
2.21-2.3170.1831030.12817180.13118210.9810.991000.114
2.317-2.4420.178870.12616650.12817520.980.991000.115
2.442-2.5890.163820.12215640.12416460.9840.9911000.114
2.589-2.7670.189820.14114820.14415640.9780.9871000.134
2.767-2.9870.178530.14514130.14614660.9830.9861000.143
2.987-3.270.184740.15612710.15813470.9780.98499.85150.159
3.27-3.6530.225620.15311600.15612260.9660.98699.67370.16
3.653-4.2110.217340.15910640.1611050.9670.98499.36650.174
4.211-5.1410.206430.1618830.1639360.9780.98598.93160.188
5.141-7.2020.242250.2347130.2347520.9680.97398.13830.269
7.202-37.1360.352210.2654240.2684640.8990.95995.90520.348

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