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- PDB-8q20: Crystal structure of Vanadium-dependent haloperoxidase R425D muta... -

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Basic information

Entry
Database: PDB / ID: 8q20
TitleCrystal structure of Vanadium-dependent haloperoxidase R425D mutant (A. marina)
ComponentsVanadium-dependent bromoperoxidase, putative
KeywordsOXIDOREDUCTASE / Vanadium / Enzyme Catalysis / Peroxidase / Halogenation / Mutant
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: 3.5 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: to be published
Title: Unraveling the Molecular Basis of Substrate Specificity and Halogen Activation in Vanadium-Dependent Haloperoxidases
Authors: Zeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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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)73,2603
Polymers73,0691
Non-polymers1912
Water00
1
A: Vanadium-dependent bromoperoxidase, putative
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)879,11536
Polymers876,82212
Non-polymers2,29224
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 area96890 Å2
ΔGint-621 kcal/mol
Surface area214600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)308.380, 308.380, 308.380
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: 73068.539 Da / Num. of mol.: 1 / Mutation: R452D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acaryochloris marina (bacteria) / Gene: AM1_4975 / Plasmid: pET28b / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 4.18 Å3/Da / Density % sol: 70.58 %
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

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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: 3.5→30 Å / Num. obs: 15830 / % possible obs: 96.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.4
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.632 / Num. unique obs: 1244 / % possible all: 96.6

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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: 3.5→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.926 / SU B: 54.558 / SU ML: 0.361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 790 5 %RANDOM
Rwork0.2243 ---
obs0.2253 15012 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.04 Å2 / Biso mean: 96.498 Å2 / Biso min: 81.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 10 0 4886
Biso mean--112.54 --
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174473
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.6436782
X-RAY DIFFRACTIONr_angle_other_deg1.0521.57610413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8755630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96923.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10315794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7851531
X-RAY DIFFRACTIONr_chiral_restr0.0370.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
X-RAY DIFFRACTIONr_rigid_bond_restr0.07239465
LS refinement shellResolution: 3.5→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 56 -
Rwork0.339 1057 -
all-1113 -
obs--96.53 %
Refinement TLS params.Method: refined / Origin x: 19.9442 Å / Origin y: 4.7943 Å / Origin z: 44.8523 Å
111213212223313233
T0.0344 Å2-0.0178 Å2-0.008 Å2-0.0139 Å20.0005 Å2--0.0089 Å2
L0.1768 °2-0.1152 °2-0.0235 °2-0.1399 °20.0174 °2--0.0827 °2
S0.02 Å °-0.0144 Å °0.0033 Å °0.0247 Å °-0.0142 Å °0.0011 Å °0.0127 Å °0.0099 Å °-0.0058 Å °

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