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- PDB-8s6c: Crystal structure of Cyanobacterium TDX16 peroxidase -

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Basic information

Entry
Database: PDB / ID: 8s6c
TitleCrystal structure of Cyanobacterium TDX16 peroxidase
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / heme
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciescyanobacterium TDX16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRozeboom, H.J. / Savino, S. / Fraaije, M.W.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Chembiochem / Year: 2025
Title: Biochemical and Structural Characterisation of a Bacterial Lactoperoxidase.
Authors: Pecanac, O. / Martin, C. / Savino, S. / Rozeboom, H.J. / Fraaije, M.W. / Loncar, N.
History
DepositionFeb 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _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: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6386
Polymers56,8251
Non-polymers8135
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, and dynamic light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-38 kcal/mol
Surface area18800 Å2
Unit cell
Length a, b, c (Å)52.667, 72.541, 56.203
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lactoperoxidase


Mass: 56825.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) cyanobacterium TDX16 (bacteria) / Production host: Escherichia coli (E. coli) / References: peroxidase

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Non-polymers , 5 types, 368 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG6000, MES buffer, Magnesium chloride or Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.737→55.91 Å / Num. obs: 42540 / % possible obs: 97.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.047 / Net I/σ(I): 9.2
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 5.7 % / Num. unique obs: 2171 / CC1/2: 0.419 / Rpim(I) all: 0.832 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→55.91 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 6.33 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18784 2072 4.9 %RANDOM
Rwork0.15088 ---
obs0.15269 40436 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.798 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20.29 Å2
2---0.93 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.74→55.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 52 363 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124148
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163804
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.7945662
X-RAY DIFFRACTIONr_angle_other_deg0.721.7498721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.778529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85310629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025148
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021003
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_it2.0712.6482129
X-RAY DIFFRACTIONr_mcbond_other2.072.6482129
X-RAY DIFFRACTIONr_mcangle_it2.9864.7512670
X-RAY DIFFRACTIONr_mcangle_other2.9864.7532671
X-RAY DIFFRACTIONr_scbond_it2.7022.8712019
X-RAY DIFFRACTIONr_scbond_other2.7022.8712020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9465.1892993
X-RAY DIFFRACTIONr_long_range_B_refined5.21928.54917
X-RAY DIFFRACTIONr_long_range_B_other5.10626.814832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.782 Å
RfactorNum. reflection% reflection
Rfree0.316 145 -
Rwork0.343 3031 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 11.4349 Å / Origin y: 0.495 Å / Origin z: 21.6339 Å
111213212223313233
T0.0036 Å2-0.0007 Å20.0004 Å2-0.0005 Å20.0004 Å2--0.0083 Å2
L0.037 °2-0.0031 °2-0.015 °2-0.0666 °20.0021 °2--0.2707 °2
S0.0055 Å °-0.004 Å °-0.0074 Å °-0.0088 Å °-0.001 Å °-0.0019 Å °-0.0233 Å °0.0047 Å °-0.0045 Å °

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