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- PDB-1vnf: CHLOROPEROXIDASE FROM THE FUNGUS CURVULARIA INAEQUALIS: MUTANT R360A -

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Basic information

Entry
Database: PDB / ID: 1vnf
TitleCHLOROPEROXIDASE FROM THE FUNGUS CURVULARIA INAEQUALIS: MUTANT R360A
ComponentsVANADIUM CHLOROPEROXIDASE
KeywordsHALOPEROXIDASE / VANADIUM-CONTAINING HALOPEROXIDASE / OXIDOREDUCTASE / MUTANT R360A
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 / OTHER / Resolution: 2.35 Å
AuthorsMacedo-Ribeiro, S. / Messerschmidt, A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 1999
Title: X-ray crystal structures of active site mutants of the vanadium-containing chloroperoxidase from the fungus Curvularia inaequalis.
Authors: Macedo-Ribeiro, S. / Hemrika, W. / Renirie, R. / Wever, R. / Messerschmidt, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: X-Ray Structure of a Vanadium-Containing Enzyme: Chloroperoxidase from the Fungus Curvularia Inaequalis
Authors: Messerschmidt, A. / Wever, R.
History
DepositionJan 20, 1999Processing site: BNL
Revision 1.0Aug 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Advisory / Database references / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)67,6562
Polymers67,5411
Non-polymers1151
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.640, 131.640, 112.850
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-1161-

HOH

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Components

#1: Protein VANADIUM CHLOROPEROXIDASE


Mass: 67541.328 Da / Num. of mol.: 1 / Mutation: R360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Curvularia inaequalis (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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.: 232 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
25 mMMOPS1drop
31 mMvanadate1drop
40.85 Mammonium sulfate1reservoir
50.05 MTris-H2SO41reservoir
60.5 mg/mlsodium vanadate1reservoir
70.05 Ml-cysteine1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
DetectorDate: Jun 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→15 Å / Num. obs: 30310 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 267056 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.39

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.35→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 -5 %RANDOM
Rwork0.19 ---
obs0.19 29585 --
Displacement parametersBiso mean: 30.86 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.35→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 5 232 4715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.48 Å / Rfactor Rfree: 0.324 / Rfactor obs: 0.325

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