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

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Basic information

Entry
Database: PDB / ID: 4usz
TitleCrystal structure of the first bacterial vanadium dependant iodoperoxidase
ComponentsVANADIUM-DEPENDENT HALOPEROXIDASE
KeywordsOXIDOREDUCTASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJul 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: VANADIUM-DEPENDENT HALOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6333
Polymers51,4951
Non-polymers1382
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.840, 85.870, 116.090
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 DEPENDANT IODOPEROXIDASE


Mass: 51495.078 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, EC: 1.11.1.8, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / 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: 2.19 Å3/Da / Density % sol: 44 %
Description: THIS IS THE NATIVE DATA, WHILE THE STRUCTURE 4CIT CONCERNS THE SE-MET LABELED PROTEIN
Crystal growpH: 7.2
Details: DROPS: 1 MICROL OF ENZYME AND % 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: BM30A / Wavelength: 1.04
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2→69.1 Å / Num. obs: 34478 / % possible obs: 99.6 % / Observed criterion σ(I): 0.1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.56 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CIT

4cit


Resolution: 2→69.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.172 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.15 / 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
Rfree0.20717 1504 5.1 %RANDOM
Rwork0.15829 ---
obs0.16075 28183 99.76 %-
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: 16.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.27 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→69.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 6 283 3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.023374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0241.9494597
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.27224.359156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53615540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2531517
X-RAY DIFFRACTIONr_chiral_restr0.1470.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212608
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 114 -
Rwork0.181 1864 -
obs--99.85 %

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