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- PDB-1pa2: ARABIDOPSIS THALIANA PEROXIDASE A2 -

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Basic information

Entry
Database: PDB / ID: 1pa2
TitleARABIDOPSIS THALIANA PEROXIDASE A2
ComponentsPEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIDASE
Function / homology
Function and homology information


defense response to nematode / flower development / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / Golgi apparatus / extracellular region / metal ion binding
Similarity search - Function
Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase 53
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHenriksen, A.
Citation
Journal: Plant Mol.Biol. / Year: 2000
Title: Arabidopsis ATP A2 peroxidase. Expression and high-resolution structure of a plant peroxidase with implications for lignification.
Authors: Ostergaard, L. / Teilum, K. / Mirza, O. / Mattsson, O. / Petersen, M. / Welinder, K.G. / Mundy, J. / Gajhede, M. / Henriksen, A.
#1: Journal: FEBS Lett. / Year: 1996
Title: Structure and Organ Specificity of an Anionic Peroxidase from Arabidopsis Thaliana Cell Suspension Culture
Authors: Ostergaard, L. / Abelskov, A.K. / Mattsson, O. / Welinder, K.G.
History
DepositionMay 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8065
Polymers32,0861
Non-polymers7214
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.156, 74.597, 80.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEROXIDASE / ATP A2


Mass: 32085.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q42578, peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.98 mg/mlprotein1drop
20.1 Mmagnesium acetate1drop
30.5 Mcacodylate1drop
410 %(w/v)PEG80001drop
50.2 Mmagnesium acetate1reservoir
60.1 Mcacodylate1reservoir
720 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→99 Å / Num. obs: 49745 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.058 / Net I/σ(I): 19.1
Reflection shellResolution: 1.45→1.51 Å / Redundancy: 4 % / Mean I/σ(I) obs: 8.4 / Rsym value: 0.202 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 99 Å / % possible obs: 99 % / Num. measured all: 280003 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 99 % / Num. unique obs: 5403 / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATJ

1atj


Resolution: 1.45→99 Å / Num. parameters: 11562 / Num. restraintsaints: 9824 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 2259 5 %RANDOM
obs0.1477 -99 %-
all-43009 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 2187 / Occupancy sum non hydrogen: 2775
Refinement stepCycle: LAST / Resolution: 1.45→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 46 471 2766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.008
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 99 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor all: 0.1477 / Rfactor obs: 0.1398
Solvent computation
*PLUS
Displacement parameters
*PLUS

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