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- PDB-5aa6: Homohexameric Structure of the second Vanadate-Dependent Bromoper... -

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Basic information

Entry
Database: PDB / ID: 5aa6
TitleHomohexameric Structure of the second Vanadate-Dependent Bromoperoxidase (AnII) from Ascophyllum nodosum
ComponentsVANADIUM-DEPENDENT BROMOPEROXIDASE 2
KeywordsOXIDOREDUCTASE / BROWN ALGAE / BROMOPEROXIDASE / VANADIUM-DEPENDANT HALOGENPEROXIDASE
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 / VANADATE ION / Vanadium-dependent bromoperoxidase 2
Function and homology information
Biological speciesASCOPHYLLUM NODOSUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRadlow, M. / Jeudy, A. / Dabin, J. / Delage, L. / Leblanc, C. / Hartung, J. / Czjzek, M.
Citation
Journal: To be Published
Title: Homohexameric Structure of the Second Vanadate Dependant Bromoperoxidase from Ascophyllum Nodosum
Authors: Radlow, M. / Czjzek, M. / Jeudy, A. / Dabin, J. / Delage, L. / Leblanc, C. / Hartung, J.
#1: Journal: Bioorg.Chem. / Year: 2012
Title: Molecular Cloning, Structure, and Reactivity of the Second Bromoperoxidase from Ascophyllum Nodosum.
Authors: Wischang, D. / Radlow, M. / Schulz, H. / Vilter, H. / Viehweger, L. / Altmeyer, M.O. / Kegler, C. / Herrmann, J. / Muller, R. / Gaillard, F. / Delage, L. / Leblanc, C. / Hartung, J.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
B: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
C: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
D: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
E: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
F: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,14812
Polymers391,4586
Non-polymers6906
Water36,1562007
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49200 Å2
ΔGint-216.1 kcal/mol
Surface area110310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.790, 236.840, 118.000
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.52, 0.036, -0.853), (-0.786, -0.372, -0.495), (-0.335, 0.928, -0.165)15.049, 18.062, 14.898
2given(-0.529, 0.801, 0.279), (0.787, 0.341, 0.515), (0.318, 0.492, -0.811)-45.006, 8.054, 50.106
3given(0.513, -0.804, -0.3), (0.018, -0.34, 0.94), (-0.858, -0.487, -0.16)10.484, -9.112, 23.538
4given(-0.502, -0.02, 0.865), (0.004, -1, -0.02), (0.865, -0.007, 0.502)-50.045, 26.141, 28.732
5given(-1, -0.026, 0.018), (-0.026, 0.355, -0.934), (0.018, -0.934, -0.356)-34.952, 34.952, 50.515
6given(-0.999527, -0.025133, 0.017739), (-0.02553, 0.355967, -0.93415), (0.017164, -0.93416, -0.356441)-34.98585, 34.11007, 50.53286

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Components

#1: Protein
VANADIUM-DEPENDENT BROMOPEROXIDASE 2


Mass: 65243.051 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: VANADATE COFACTOR LINKED TO HISTIDINE 536 IN ALL CHAINS. THE BIOLOGICAL MACROMOLECULE HAS THE HOMOHEXAMERIC FORM PRESENT IN THE CRYSTAL STRUCTURE
Source: (natural) ASCOPHYLLUM NODOSUM (eukaryote) / Tissue: CELL WALL (EXTRACELLULAR MATRIX) / References: UniProt: K7ZUA3, bromide peroxidase
#2: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2007 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsVANADATE (VO4): THE VANADATE IS COORDINATED BY HIS 536
Sequence detailsTHE CRYSTAL STRUCTURE CONTAINS A NATIVE PURIFIED PROTEIN FROM THE ORGANISM. THIS FAMILY OF ENZYMES ...THE CRYSTAL STRUCTURE CONTAINS A NATIVE PURIFIED PROTEIN FROM THE ORGANISM. THIS FAMILY OF ENZYMES IS KNOWN TO DISPLAY MANY ISO-FORMS. THE DEDUCED SEQUENCE FROM THE CRYSTAL STRUCTURE DISPLAYS FEW BUT REAL DISCREPANCIES TO THE DEPOSITED SEQUENCE AT UNIPROT

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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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP AT 18 DEGREES C, 2 MICROL OF PROTEIN WITH 1 MICROL RESERVOIR SOLUTION, NACL 0.1 M, BIS-TRIS 0.01 M, PH 5.5 AND 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.26→65 Å / Num. obs: 170315 / % possible obs: 98.7 % / Observed criterion σ(I): 0.1 / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QI9

1qi9


Resolution: 2.26→70 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.107 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WERE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23592 8509 5 %RANDOM
Rwork0.16987 ---
obs0.17317 161755 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-1.53 Å2
2---1.25 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.26→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27293 0 30 2007 29330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01928461
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9638803
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04453714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24124.6031349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.712154549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.70215175
X-RAY DIFFRACTIONr_chiral_restr0.1040.24250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122251
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 590 -
Rwork0.258 11815 -
obs--98.48 %

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