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- PDB-1idu: CRYSTAL STRUCTURE OF THE PEROXIDE FORM OF THE VANADIUM-CONTAINING... -

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Basic information

Entry
Database: PDB / ID: 1idu
TitleCRYSTAL STRUCTURE OF THE PEROXIDE FORM OF THE VANADIUM-CONTAINING CHLOROPEROXIDASE FROM CURVULARIA INAEQUALIS
ComponentsVANADIUM CHLOROPEROXIDASE
KeywordsOXIDOREDUCTASE / Two four-helix bundles / peroxide derivative
Function / homology
Function and homology information


chloride peroxidase / chloride peroxidase activity / extracellular region / metal ion binding
Similarity search - Function
Vanadium chloroperoxidase, N-terminal / Vanadium chloroperoxidase N-terminal domain / Vanadium-containing Chloroperoxidase, domain 2 / Vanadium-containing Chloroperoxidase; domain 2 / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / Bromoperoxidase/chloroperoxidase C-terminal / : / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily ...Vanadium chloroperoxidase, N-terminal / Vanadium chloroperoxidase N-terminal domain / Vanadium-containing Chloroperoxidase, domain 2 / Vanadium-containing Chloroperoxidase; domain 2 / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / Bromoperoxidase/chloroperoxidase C-terminal / : / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
VANADATE ION / Vanadium chloroperoxidase
Similarity search - Component
Biological speciesCurvularia inaequalis (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.24 Å
AuthorsMesserschmidt, A. / Prade, L. / Wever, R.
CitationJournal: Biol.Chem. / Year: 1997
Title: Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the fungus Curvularia inaequalis by X-ray structures of the native and peroxide form.
Authors: Messerschmidt, A. / Prade, L. / Wever, R.
History
DepositionApr 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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 CHLOROPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7182
Polymers67,6031
Non-polymers1151
Water10,881604
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.950, 129.950, 111.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2024-

HOH

21A-2031-

HOH

DetailsThe biologically active molecule is a monomer.

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Components

#1: Protein VANADIUM CHLOROPEROXIDASE / VCPO / VANADIUM CHLORIDE PEROXIDASE


Mass: 67603.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Curvularia inaequalis (fungus)
Strain: STRAIN 102.42 FROM CENTRAAL BUREAU VOR SCHIMMELCULTURES (CBS, BAARN, THE NETHERLANDS)
References: UniProt: P49053, chloride peroxidase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir: 1.5 M ammonium sulfate, 0.1 M Tris-HCl; protein drop: 7.5 microliter protein solution (8.7 mg/ml), 1 mM Na3VO4 plus 2.5 microliter reservoir solution. The peroxide complex was ...Details: Reservoir: 1.5 M ammonium sulfate, 0.1 M Tris-HCl; protein drop: 7.5 microliter protein solution (8.7 mg/ml), 1 mM Na3VO4 plus 2.5 microliter reservoir solution. The peroxide complex was produced by soaking the crystals in mother liquor (2M ammonium sulfate, 0.1 M Tris-H2SO4, pH 8.0), containing 20 mM peroxide, for two hours and then flash cooled., VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlprotein1drop
23.75 mMMops1drop
30.75 M1dropNa3VO4
40.375 Mammonium sulfate1drop
50.025 MTris-HCl1drop
60.005 %1dropNaN3
71.6 Mammonium sulfate1reservoir
80.1 MTris-HCl1reservoir
90.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1996 / Details: Graphite monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.24→33.84 Å / Num. all: 33853 / Num. obs: 29878 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.114 / Net I/σ(I): 7.5
Reflection shellResolution: 2.24→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3750 / Rsym value: 0.293 / % possible all: 40.2
Reflection
*PLUS
Num. measured all: 102166
Reflection shell
*PLUS
% possible obs: 40.2 %

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Processing

Software
NameVersionClassification
CCP4:SFCALCmodel building
FFTmodel building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
SFCALCphasing
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1VNC

1vnc


Resolution: 2.24→8 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.177 --
all-33172 -
obs-29291 88.3 %
Displacement parametersBiso mean: 29.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.24→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 5 604 5096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.605
X-RAY DIFFRACTIONc_dihedral_angle_d23.17
X-RAY DIFFRACTIONc_improper_angle_d1.5
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
2.24-2.340.2972X-RAY DIFFRACTION3685
2.34-2.460.2393X-RAY DIFFRACTION3741
2.46-2.610.213X-RAY DIFFRACTION3705
2.61-2.80.1978X-RAY DIFFRACTION3713
2.8-3.070.1739X-RAY DIFFRACTION3673
3.07-3.480.1517X-RAY DIFFRACTION3676
3.48-4.270.1261X-RAY DIFFRACTION3584
4.27-80.1601X-RAY DIFFRACTION3514
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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