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- PDB-2vnx: Crystal structure of soybean ascorbate peroxidase mutant W41A aft... -

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Basic information

Entry
Database: PDB / ID: 2vnx
TitleCrystal structure of soybean ascorbate peroxidase mutant W41A after exposure to a high dose of x-rays
ComponentsASCORBATE PEROXIDASE
KeywordsOXIDOREDUCTASE / APX / PEROXIDASE / HEME ENZYME / REDUCTION BY X-RAYS
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / 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
PROTOPORPHYRIN IX CONTAINING FE / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMetcalfe, C.L. / Badyal, S.K. / Raven, E.L. / Moody, P.C.E.
CitationJournal: Biochemistry / Year: 2008
Title: Iron Oxidation State Modulates Active Site Structure in a Heme Peroxidase.
Authors: Badyal, S.K. / Metcalfe, C.L. / Basran, J. / Efimov, I. / Moody, P.C.E. / Raven, E.L.
History
DepositionFeb 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Assembly

Deposited unit
X: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8863
Polymers28,2471
Non-polymers6392
Water5,675315
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.002, 82.002, 75.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11X-2056-

HOH

21X-2156-

HOH

31X-2259-

HOH

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Components

#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: HISTIDINE 42 IS IN A DUAL CONFORMATION RESULTING IN A MOVEMENT OF RESIDUES 40-45.
Source: (gene. exp.) GLYCINE MAX (soybean) / Plasmid: SOYAPX/W41A / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): SG13009 / References: UniProt: Q43758, EC: 1.11.11.1
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN X, TRP 41 TO ALA

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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: 1.97 Å3/Da / Density % sol: 37.13 % / Description: NONE
Crystal growpH: 8.3 / Details: pH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→37.8 Å / Num. obs: 34661 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 10.18 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 9.89 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

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

2ggn


Resolution: 1.5→37.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.889 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2113 5 %RANDOM
Rwork0.175 ---
obs0.177 39733 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 44 315 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222049
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1522.0442804
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9765266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67324.09683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23915314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.562159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021599
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21093
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21398
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8241.51286
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34822054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9583786
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9494.5746
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 163
Rwork0.265 2885

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