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- PDB-1vnc: CHLOROPEROXIDASE FROM THE FUNGUS CURVULARIA INAEQUALIS -

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Basic information

Entry
Database: PDB / ID: 1vnc
TitleCHLOROPEROXIDASE FROM THE FUNGUS CURVULARIA INAEQUALIS
ComponentsVANADIUM-CONTAINING CHLOROPEROXIDASE
KeywordsOXIDOREDUCTASE / VANADIUM-CONTAINING HALOPEROXIDASE
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
AZIDE ION / VANADATE ION / Vanadium chloroperoxidase
Similarity search - Component
Biological speciesCurvularia inaequalis (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMesserschmidt, A. / Wever, R.
CitationJournal: 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
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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-CONTAINING CHLOROPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7843
Polymers67,6271
Non-polymers1572
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VANADIUM-CONTAINING CHLOROPEROXIDASE
hetero molecules

A: VANADIUM-CONTAINING CHLOROPEROXIDASE
hetero molecules

A: VANADIUM-CONTAINING CHLOROPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,3539
Polymers202,8823
Non-polymers4716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6320 Å2
ΔGint-32 kcal/mol
Surface area60990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.690, 131.690, 112.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein VANADIUM-CONTAINING CHLOROPEROXIDASE


Mass: 67627.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Curvularia inaequalis (fungus) / 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: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 41486 / % possible obs: 98.9 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 42197 / Num. measured all: 132089 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.14 Å / % possible obs: 96.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 41486 98.5 %
Displacement parametersBiso mean: 20.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 7 429 4920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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