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- PDB-1apx: CRYSTAL STRUCTURE OF RECOMBINANT ASCORBATE PEROXIDASE -

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Basic information

Entry
Database: PDB / ID: 1apx
TitleCRYSTAL STRUCTURE OF RECOMBINANT ASCORBATE PEROXIDASE
ComponentsCYTOSOLIC ASCORBATE PEROXIDASE
KeywordsPEROXIDASE
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm
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, cytosolic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPatterson, W.R. / Poulos, T.L.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure of recombinant pea cytosolic ascorbate peroxidase.
Authors: Patterson, W.R. / Poulos, T.L.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Characterization and Crystallization of Recombinant Pea Cytosolic Ascorbate Peroxidase
Authors: Patterson, W.R. / Poulos, T.L.
History
DepositionFeb 1, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: CYTOSOLIC ASCORBATE PEROXIDASE
B: CYTOSOLIC ASCORBATE PEROXIDASE
C: CYTOSOLIC ASCORBATE PEROXIDASE
D: CYTOSOLIC ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,01312
Polymers108,3904
Non-polymers2,6228
Water11,620645
1
A: CYTOSOLIC ASCORBATE PEROXIDASE
B: CYTOSOLIC ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5066
Polymers54,1952
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CYTOSOLIC ASCORBATE PEROXIDASE
D: CYTOSOLIC ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5066
Polymers54,1952
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.400, 53.000, 170.600
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.084667, -0.87086, 0.484183), (-0.882381, -0.291255, -0.369558), (0.462855, -0.395945, -0.793091)-10.46655, -1.28575, 22.32684
2given(0.718692, 0.609492, -0.334665), (-0.624032, 0.777675, 0.076196), (0.306702, 0.154081, 0.939252)19.4881, 24.8207, 41.36917
3given(-0.634598, -0.681811, 0.363894), (-0.689757, 0.28728, -0.66461), (0.348599, -0.672758, -0.652591)4.00326, 32.5688, 58.65225
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 2 .. A 250 B 2 .. B 250 0.321 M2 A 2 .. A 250 C 2 .. C 250 0.347 M3 A 2 .. A 250 D 2 .. D 250 0.280

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Components

#1: Protein
CYTOSOLIC ASCORBATE PEROXIDASE


Mass: 27097.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: P48534, L-ascorbate peroxidase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop / Details: or 7 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 %PEG40001reservoir
30.2 Msodium acetate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 8, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 65092 / % possible obs: 72 % / Observed criterion σ(I): 2 / Redundancy: 2.6 %
Reflection
*PLUS
Lowest resolution: 9999 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENV. 2.0data reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 2
Details: THE ALA 250 RESIDUES, PLUS THE C-TERMINAL CARBOXYL GROUP, WERE ROUGHLY MODELED INTO POOR, BUT OBSERVABLE, DENSITY.
RfactorNum. reflection% reflection
Rwork0.193 --
obs0.193 51337 91 %
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7660 0 176 645 8481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.279

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