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- PDB-3bb0: Crystal Structure of a Trapped Phosphate-Intermediate in Vanadium... -

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Basic information

Entry
Database: PDB / ID: 3bb0
TitleCrystal Structure of a Trapped Phosphate-Intermediate in Vanadium Apochloroperoxidase Catalyzing a Dephosphorylation Reaction
ComponentsVanadium chloroperoxidase
KeywordsOXIDOREDUCTASE / Protein phosphate-intermediate complex / phospatase activity / Chloride / Metal-binding / Peroxidase / Secreted / Vanadium
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
PHOSPHITE ION / Vanadium chloroperoxidase
Similarity search - Component
Biological speciesCurvularia inaequalis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMesserschmidt, A. / Macedo-Ribeiro, S.
Citation
Journal: Biochemistry / Year: 2008
Title: Crystal structure of a trapped phosphate intermediate in vanadium apochloroperoxidase catalyzing a dephosphorylation reaction
Authors: Macedo-Ribeiro, S. / 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.
#2: 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.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)67,9434
Polymers67,6721
Non-polymers2713
Water14,322795
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.060, 128.060, 103.310
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-1003-

HOH

21A-1029-

HOH

31A-1656-

HOH

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Components

#1: Protein Vanadium chloroperoxidase / VCPO / Vanadium chloride peroxidase


Mass: 67671.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Curvularia inaequalis (fungus) / Gene: CPO / Plasmid: pTNT14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ1991 / References: UniProt: P49053, chloride peroxidase
#2: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONFLICT MAY BE A SEQUENCING ERROR (THE CODON FOR ARG VARIES BY ONE NUCLEOTIDE CHANGE WITH PRO ...THIS CONFLICT MAY BE A SEQUENCING ERROR (THE CODON FOR ARG VARIES BY ONE NUCLEOTIDE CHANGE WITH PRO ONLY) OR AN INCORRECT READING OF THE RNA-POLYMERASE. IN PDB ENTRIES 1VNC AND 1VNS THE RESIDUE WAS DETERMINED AS GLUTAMATE FROM THE X-RAY STRUCTURES BUT THE RESOLUTION OF THIS STRUCTURE DETERMINATION IS BETTER AND IDENTIFIES THE RESIDUE UNAMBIGUOUSLY AS ARGININE.

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3 micro-l of protein solution (5mg/ml in 5mM MOPS, pH 7.5), 3 micro-l precipitating buffer (1.7M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, 0.3 micro-l 10mM cysteine-HCl) , VAPOR DIFFUSION, ...Details: 3 micro-l of protein solution (5mg/ml in 5mM MOPS, pH 7.5), 3 micro-l precipitating buffer (1.7M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, 0.3 micro-l 10mM cysteine-HCl) , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 1998 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 101188 / Num. obs: 100278 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 8.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5046 / Rsym value: 0.317 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345Imageplate softwaredata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VNS

1vns


Resolution: 1.5→14.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.066 / SU ML: 0.041 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19391 5076 5.1 %RANDOM
Rwork0.17283 ---
obs0.17391 95202 100 %-
all-96066 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.08 Å0.071 Å
Luzzati d res low-5 Å
Luzzati sigma a0.085 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 14 796 5308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224643
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9516346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2355.035577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55823.656227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8115669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1281535
X-RAY DIFFRACTIONr_chiral_restr0.0860.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023712
X-RAY DIFFRACTIONr_nbd_refined0.1960.22244
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2531
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.273
X-RAY DIFFRACTIONr_mcbond_it0.7151.52947
X-RAY DIFFRACTIONr_mcangle_it1.14224662
X-RAY DIFFRACTIONr_scbond_it1.64331925
X-RAY DIFFRACTIONr_scangle_it2.4294.51684
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 363 -
Rwork0.197 6883 -
obs--100 %

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