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- PDB-5lpc: Crystal structure of Vanadium-dependent Haloperoxidase from A. marina -

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Basic information

Entry
Database: PDB / ID: 5lpc
TitleCrystal structure of Vanadium-dependent Haloperoxidase from A. marina
ComponentsVanadium-dependent bromoperoxidase
KeywordsOXIDOREDUCTASE / Vanadium / Enzyme Catalysis / Peroxidase / Halogenation
Function / homologyVanadium-containing Chloroperoxidase, domain 2 / Vanadium-containing Chloroperoxidase; domain 2 / Bromoperoxidase/chloroperoxidase C-terminal / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / peroxidase activity / Orthogonal Bundle / Mainly Alpha / PHOSPHATE ION / Vanadium-dependent bromoperoxidase, putative
Function and homology information
Biological speciesAcaryochloris marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFrank, A. / Groll, M.
CitationJournal: Chembiochem / Year: 2016
Title: Characterization of a Cyanobacterial Haloperoxidase and Evaluation of its Biocatalytic Halogenation Potential.
Authors: Frank, A. / Seel, C.J. / Groll, M. / Gulder, T.
History
DepositionAug 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vanadium-dependent bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1652
Polymers73,0701
Non-polymers951
Water00
1
A: Vanadium-dependent bromoperoxidase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)877,97524
Polymers876,83512
Non-polymers1,14012
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 area80290 Å2
ΔGint-471 kcal/mol
Surface area211510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)306.160, 306.160, 306.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein Vanadium-dependent bromoperoxidase


Mass: 73069.617 Da / Num. of mol.: 1
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

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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: 4.09 Å3/Da / Density % sol: 69.93 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2015
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 21760 / % possible obs: 95.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.2 Å / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UP8

1up8


Resolution: 3.1→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 37.173 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 1.23 / ESU R Free: 0.386 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24941 1088 5 %RANDOM
Rwork0.20745 ---
obs0.20949 20672 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.951 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 5 0 4816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194924
X-RAY DIFFRACTIONr_bond_other_d0.0010.024586
X-RAY DIFFRACTIONr_angle_refined_deg0.9091.9596686
X-RAY DIFFRACTIONr_angle_other_deg0.703310543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.665622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02724.59244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71815781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2121532
X-RAY DIFFRACTIONr_chiral_restr0.0480.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021153
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9777.1862494
X-RAY DIFFRACTIONr_mcbond_other0.9777.1862493
X-RAY DIFFRACTIONr_mcangle_it1.7310.7773114
X-RAY DIFFRACTIONr_mcangle_other1.7310.7773115
X-RAY DIFFRACTIONr_scbond_it0.7647.2092429
X-RAY DIFFRACTIONr_scbond_other0.7637.212425
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.36310.7913566
X-RAY DIFFRACTIONr_long_range_B_refined2.73156.6155591
X-RAY DIFFRACTIONr_long_range_B_other2.7356.6185592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.101→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 75 -
Rwork0.387 1438 -
obs--94.74 %
Refinement TLS params.Method: refined / Origin x: 20.3717 Å / Origin y: 4.521 Å / Origin z: 44.5459 Å
111213212223313233
T0.0761 Å2-0.0593 Å2-0.0371 Å2-0.0866 Å20.0046 Å2--0.036 Å2
L0.3958 °2-0.051 °2-0.0794 °2-0.2327 °2-0.0124 °2--0.1712 °2
S0.0673 Å °-0.057 Å °0.0015 Å °0.06 Å °-0.053 Å °-0.0266 Å °-0.0096 Å °0.0287 Å °-0.0143 Å °

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