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- PDB-2wd4: Ascorbate Peroxidase as a heme oxygenase: w41A variant product wi... -

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Basic information

Entry
Database: PDB / ID: 2wd4
TitleAscorbate Peroxidase as a heme oxygenase: w41A variant product with t-butyl peroxide
ComponentsASCORBATE PEROXIDASE
KeywordsOXIDOREDUCTASE / TERT-BUTYL PEROXIDE / HEME PEROXIDASE / PEROXIDE SCAVENGE
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-TBV / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBadyal, S.K. / Metcalfe, C.L. / Gumiero, A. / Raven, E.L. / Moody, P.C.E.
CitationJournal: Biochemistry / Year: 2009
Title: Evidence for Heme Oxygenase Activity in a Heme Peroxidase.
Authors: Raven, E.L. / Badyal, S.K. / Eaton, G. / Mistry, S. / Pipirou, Z. / Basran, J. / Metcalfe, C.L. / Gumiero, A. / Handa, S. / Moody, P.C.E.
History
DepositionMar 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1616
Polymers28,2471
Non-polymers9145
Water3,405189
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.067, 82.067, 75.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ASCORBATE PEROXIDASE / CYTOSOLIC ASCORBATE PEROXIDASE 1


Mass: 28246.775 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-250 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: REACTION PRODUCT WITH T-BUTYL PEROXIDE SHOWING HEME OXYGENASE ACTIVITY FORM BILIVERDIN DERIVATIVE
Source: (gene. exp.) GLYCINE MAX (soybean) / Plasmid: PAPX4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: Q43758, L-ascorbate peroxidase

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TBV / 3-[2-[[3-(2-CARBOXYETHYL)-5-[[3-ETHENYL-4-METHYL-5-[(2-METHYLPROPAN-2-YL)OXY]-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL -2-YL]METHYL]-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXO-PYRROL-2-YLIDENE)METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID / BILIVERDIN


Mass: 642.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H46N4O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 41 TO ALA
Nonpolymer detailsTERT BUTYL BILIVERDIN (TBV): PRODUCT OF REACTION BETWEEN HEME AND TERT BUTYL PEROXIDE

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP, LI2SO4 2.25 M, HEPES 0.1 M PH 8.3, PROTEIN CONCENTRATION 10 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 2, 2007 / Details: HORIZONTALLY BENDED GE(220)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→82.2 Å / Num. obs: 51023 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.5
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GGN

2ggn


Resolution: 1.4→58.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.18 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21638 2585 5.1 %RANDOM
Rwork0.18973 ---
obs0.1911 48382 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.4→58.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 59 189 2138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.622.0142869
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7435274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95924.48387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20615333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.585159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21061
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7361.51296
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23722089
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.113833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1984.5772
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: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 173 -
Rwork0.232 3529 -
obs--99.97 %

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