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- PDB-8q22: Crystal structure of Vanadium-dependent haloperoxidase R425S muta... -

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Basic information

Entry
Database: PDB / ID: 8q22
TitleCrystal structure of Vanadium-dependent haloperoxidase R425S mutant in complex with 1,3,5-trimethoxybenzene (A. marina)
ComponentsVanadium-dependent bromoperoxidase, putative
KeywordsOXIDOREDUCTASE / Vanadium / Enzyme Catalysis / Peroxidase / Halogenation / Mutant / Ligand-Complex
Function / homologyBromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / peroxidase activity / : / PHOSPHATE ION / Vanadium-dependent bromoperoxidase, putative
Function and homology information
Biological speciesAcaryochloris marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Unraveling the molecular basis of substrate specificity and halogen activation in vanadium-dependent haloperoxidases.
Authors: Zeides, P. / Bellmann-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schoeder, C.T. / Groll, M. / Gulder, T.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vanadium-dependent bromoperoxidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3505
Polymers73,0411
Non-polymers3094
Water00
1
A: Vanadium-dependent bromoperoxidase, putative
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)880,19660
Polymers876,48612
Non-polymers3,71048
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation82_555-y,z,-x1
Buried area107380 Å2
ΔGint-922 kcal/mol
Surface area200160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)305.800, 305.800, 305.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein Vanadium-dependent bromoperoxidase, putative


Mass: 73040.531 Da / Num. of mol.: 1 / Mutation: R452S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acaryochloris marina (bacteria) / Gene: AM1_4975 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0C4R0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ILW / 1,3,5-trimethoxybenzene


Mass: 168.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY
Has protein modificationY

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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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS, 1.25 M ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate, 10 mM 1,3,5-trimethoxybenzene

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 17934 / % possible obs: 94.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2 / Num. unique obs: 1528

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 46.631 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 895 5 %RANDOM
Rwork0.2163 ---
obs0.218 17015 94.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.82 Å2 / Biso mean: 83.809 Å2 / Biso min: 70.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 19 0 4950
Biso mean--99.72 --
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174527
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.6456871
X-RAY DIFFRACTIONr_angle_other_deg1.0461.57910534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0565638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65123.11283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08315801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9251531
X-RAY DIFFRACTIONr_chiral_restr0.0340.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021044
X-RAY DIFFRACTIONr_rigid_bond_restr0.11939585
LS refinement shellResolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 66 -
Rwork0.405 1252 -
all-1318 -
obs--95.44 %
Refinement TLS params.Method: refined / Origin x: 19.3154 Å / Origin y: 4.7758 Å / Origin z: 44.4646 Å
111213212223313233
T0.0074 Å2-0.0042 Å2-0.0057 Å2-0.0033 Å20.0024 Å2--0.0056 Å2
L0.1676 °2-0.0226 °20.0068 °2-0.0535 °2-0.0234 °2--0.1239 °2
S0.0236 Å °-0.0145 Å °-0.0119 Å °0.0069 Å °-0.0074 Å °-0.007 Å °0.0086 Å °0.0052 Å °-0.0161 Å °

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