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- PDB-4cit: Crystal structure of the first bacterial vanadium dependant iodop... -

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Basic information

Entry
Database: PDB / ID: 4cit
TitleCrystal structure of the first bacterial vanadium dependant iodoperoxidase
ComponentsVANADIUM-DEPENDENT HALOPEROXIDASE
KeywordsTRANSFERASE / IODOPEROXIDASE / MARINE BACTERIUM
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity
Similarity search - Function
Vanadium-containing Chloroperoxidase; domain 2 - #20 / Vanadium-containing Chloroperoxidase; domain 2 / Phosphatidic acid phosphatase type 2/haloperoxidase / : / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
VANADATE ION / Vanadium-dependent haloperoxidase
Similarity search - Component
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsRebuffet, E. / Delage, L. / Fournier, J.B. / Rzonca, J. / Potin, P. / Michel, G. / Czjzek, M. / Leblanc, C.
CitationJournal: Appl.Environ.Microbiol. / Year: 2014
Title: The Bacterial Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Zobellia Galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in This Enzyme Family.
Authors: Fournier, J.B. / Rebuffet, E. / Delage, L. / Grijol, R. / Meslet-Cladiere, L. / Rzonca, J. / Potin, P. / Michel, G. / Czjzek, M. / Leblanc, C.
History
DepositionDec 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jun 3, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_sheet_hbond.sheet_id ..._pdbx_database_status.status_code_sf / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn_type.id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 9, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VANADIUM-DEPENDENT HALOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1417
Polymers51,5431
Non-polymers5986
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 84.400, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VANADIUM-DEPENDENT HALOPEROXIDASE / VANADIUM DEPENDENT IODOPEROXIDASE


Mass: 51543.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VANADATE COFACTOR LINKED THROUGH HIS 416 / Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) AND AVAILABLE AT STATION BIOLOGIQUE DE ROSCOFF, FRANCE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: G0LAH5, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, EC: 1.11.1.8
#2: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE
Crystal growpH: 4.2
Details: 1 MICROL OF ENZYME AND 0.5 MICROL OF RESERVOIR SOLUTION CONTAINING 23 % PEG 1150, 100 MM PHOSPHATE/CITRATE PH 4.2 AND 2 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 198448 / % possible obs: 99.2 % / Observed criterion σ(I): 0.1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.91
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.74 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.8→20.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.789 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18034 1983 5 %RANDOM
Rwork0.13962 ---
obs0.14164 37341 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 6 307 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193418
X-RAY DIFFRACTIONr_bond_other_d0.0010.023167
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9514666
X-RAY DIFFRACTIONr_angle_other_deg1.01137322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17224.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3671518
X-RAY DIFFRACTIONr_chiral_restr0.1410.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
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: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 129 -
Rwork0.18 2539 -
obs--91.09 %

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