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- PDB-1qi9: X-RAY SIRAS STRUCTURE DETERMINATION OF A VANADIUM-DEPENDENT HALOP... -

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Basic information

Entry
Database: PDB / ID: 1qi9
TitleX-RAY SIRAS STRUCTURE DETERMINATION OF A VANADIUM-DEPENDENT HALOPEROXIDASE FROM ASCOPHYLLUM NODOSUM AT 2.0 A RESOLUTION
Components(Vanadium-dependent bromoperoxidase) x 2
KeywordsOXIDOREDUCTASE / BROMOPEROXIDASE / VANADIUM / HALOPEROXIDASE
Function / homology
Function and homology information


bromide peroxidase / bromide peroxidase activity / metal ion binding
Similarity search - Function
Vanadium-containing Chloroperoxidase, domain 2 / Vanadium-containing Chloroperoxidase; domain 2 / Bromoperoxidase/chloroperoxidase C-terminal / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
VANADATE ION / Vanadium-dependent bromoperoxidase
Similarity search - Component
Biological speciesAscophyllum nodosum (eukaryote)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.05 Å
AuthorsWeyand, M. / Hecht, H.-J. / Kiess, M. / Liaud, M.F. / Vilter, H. / Schomburg, D.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: X-ray structure determination of a vanadium-dependent haloperoxidase from Ascophyllum nodosum at 2.0 A resolution.
Authors: Weyand, M. / Hecht, H. / Kiess, M. / Liaud, M. / Vilter, H. / Schomburg, D.
History
DepositionJun 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jun 7, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / exptl_crystal_grow / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _exptl_crystal_grow.pdbx_details / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn_type.id / _struct_ref_seq.ref_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vanadium-dependent bromoperoxidase
B: Vanadium-dependent bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4274
Polymers121,1982
Non-polymers2302
Water31,6881759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-57 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.190, 113.190, 272.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Vanadium-dependent bromoperoxidase / V-BPO / Vanadium haloperoxidase


Mass: 60661.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ascophyllum nodosum (eukaryote) / References: UniProt: P81701, bromide peroxidase
#2: Protein Vanadium-dependent bromoperoxidase / V-BPO / Vanadium haloperoxidase


Mass: 60535.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ascophyllum nodosum (eukaryote) / References: UniProt: P81701, bromide peroxidase
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: VO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1759 / Source method: obtained synthetically / Formula: H2O

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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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growpH: 8 / Details: 2.0 M AMMONIUM SULPHATE, 50 MM TRIS/HCL, PH 8.0
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.9 mMTris1drop
31.9-2.1 Mammonium sulfate1reservoir
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 15, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→31.6 Å / Num. obs: 105540 / % possible obs: 95 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 1.4 % / % possible all: 85.7
Reflection
*PLUS
Num. obs: 105643
Reflection shell
*PLUS
% possible obs: 85.7 % / Num. unique obs: 13969

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Processing

Software
NameVersionClassification
X-GENdata scaling
CCP4SCALAdata reduction
REFMACrefinement
X-GENdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.05→31 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5320 5 %RANDOM
Rwork0.165 ---
obs-100219 95 %-
Displacement parametersBiso mean: 9.56 Å2
Refinement stepCycle: LAST / Resolution: 2.05→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8490 0 15 1759 10264
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2862
X-RAY DIFFRACTIONp_mcangle_it1.7353
X-RAY DIFFRACTIONp_scbond_it1.6282
X-RAY DIFFRACTIONp_scangle_it2.2553
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1170.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor14.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.820
X-RAY DIFFRACTIONp_special_tor

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