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- PDB-1oaf: Ascobate peroxidase from soybean cytosol in complex with ascorbate -

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Basic information

Entry
Database: PDB / ID: 1oaf
TitleAscobate peroxidase from soybean cytosol in complex with ascorbate
ComponentsASCORBATE PEROXIDASE
KeywordsOXIDOREDUCTASE / HEME PEROXIDASE / PEROXIDE SCAVENGE / ASCORBATE PEROXIDASE
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 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / 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
ASCORBIC ACID / PROTOPORPHYRIN IX CONTAINING FE / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSharp, K.H. / Raven, E.L. / Moody, P.C.E.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Crystal Structure of the Ascorbate Peroxidase-Ascorbate Complex
Authors: Sharp, K.H. / Mewies, M. / Moody, P.C.E. / Raven, E.L.
History
DepositionJan 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _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_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,1784
Polymers28,3621
Non-polymers8163
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.328, 81.328, 74.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ASCORBATE PEROXIDASE


Mass: 28361.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GLYCINE MAX (soybean) / Description: N-TERMINAL 6-HIS TAG / Plasmid: PAPX4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: Q43758, L-ascorbate peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 8.3 / Details: 2.25M LI2SO4, 0.1M HEPES, PH8.3, pH 8.30
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.25 Mlithium sulfate1reservoir
30.1 MHEPES1reservoirpH8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.4→54 Å / Num. obs: 49370 / % possible obs: 96.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.2
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.9 / % possible all: 96.2
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 57.74 Å / Num. measured all: 339792
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 96.2 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1APX

1apx


Resolution: 1.4→57.74 Å / SU B: 0.886 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUE 1 AND THE N-TERMINAL HIS-TAG ARE NOT VISIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.19625 2518 5.1 %RANDOM
Rwork0.16081 ---
obs0.16259 24727 99.05 %-
Displacement parametersBiso mean: 15.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 56 505 2472
Refinement
*PLUS
Highest resolution: 1.4 Å / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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