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- PDB-1qo4: ARABIDOPSIS THALIANA PEROXIDASE A2 AT ROOM TEMPERATURE -

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Basic information

Entry
Database: PDB / ID: 1qo4
TitleARABIDOPSIS THALIANA PEROXIDASE A2 AT ROOM TEMPERATURE
ComponentsPEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIDASE
Function / homology
Function and homology information


defense response to nematode / flower development / lactoperoxidase activity / peroxidase / 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 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Plant peroxidase / Secretory peroxidase / 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 / Peroxidase 53
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHenriksen, A. / Gajhede, M.
CitationJournal: Biochemistry / Year: 2001
Title: Differential Activity and Structure of Highly Similar Peroxidases. Spectroscopic, Crystallographic, and Enzymatic Analyses of Lignifying Arabidopsis Thaliana Peroxidase A2 and Horseradish Peroxidase A2
Authors: Nielsen, K.L. / Indiani, C. / Henriksen, A. / Feis, A. / Becucci, M. / Gajhede, M. / Smulevich, G. / Welinder, K.G.
History
DepositionNov 2, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2000Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 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_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.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.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

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Assembly

Deposited unit
A: PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7824
Polymers32,0861
Non-polymers6973
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.290, 74.848, 80.794
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 / MYELOPEROXIDASE


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-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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMET A 0 INSERTED AS A CLONING ARTIFACT

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5
Details: 0.2 M MG(CH3COO)2, 0.1 M CACODYLATE PH 6.5, 20 % PEG8000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Ostergaard, L., (2000) Plant Mol. Biol., 44, 231.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.98 mg/mlprotein1drop
20.1 M1dropMg(CH3COO)2
30.5 Mcacodylate1drop
410 %(w/v)PEG80001drop
50.2 M1reservoirMg(CH3COO)2
60.1 Mcacodylate1reservoir
720 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→39 Å / Num. obs: 5887 / % possible obs: 97 % / Redundancy: 4.6 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.165 / Net I/σ(I): 8
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5 / Rsym value: 0.295 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97.8 % / Num. measured all: 27478 / Rmerge(I) obs: 0.165
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.11 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PA2

1pa2


Resolution: 3→30 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 70416.12 / Cross valid method: THROUGHOUT / σ(F): 0
Details: A 3SIGMA FO-FC DENSITY APPEARS WITH A CENTER 2.5 ANGSTROM ABOVE THE HEME IRON. A WATER MOLECULE COULD NOT BE FITTED TO THIS DENSITY AS NO POSITIVE 2FO-FC ELECTRON DENSITY IS RETURNED. THE ...Details: A 3SIGMA FO-FC DENSITY APPEARS WITH A CENTER 2.5 ANGSTROM ABOVE THE HEME IRON. A WATER MOLECULE COULD NOT BE FITTED TO THIS DENSITY AS NO POSITIVE 2FO-FC ELECTRON DENSITY IS RETURNED. THE POSITIVE FO-FC DENSITY COULD ORIGINATE FROM A FRACTIONALLY OCCUPIED WATER MOLECULE. A FRACTIONALLY OCCUPIED WATER MOLECULE IS NOT INCLUDED IN THIS POSITION DUE TO THE RELATIVE LOW RESOLUTION OF THE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 314 5.6 %RANDOM
Rwork0.183 ---
obs0.183 5560 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.310099 e/Å3
Displacement parametersBiso mean: 15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 45 68 2362
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 46 5.3 %
Rwork0.22 822 -
obs--90.9 %
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
LS refinement shell
*PLUS
Lowest resolution: 3.11 Å / Rfactor Rwork: 0.22 / Rfactor obs: 0.22

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