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- PDB-1sch: PEANUT PEROXIDASE -

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Basic information

Entry
Database: PDB / ID: 1sch
TitlePEANUT PEROXIDASE
ComponentsPEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
KeywordsOXIDOREDUCTASE / CALCIUM BINDING / GLYCOSYLATION / PEROXIDASE
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / 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 / Cationic peroxidase 1
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / Resolution: 2.56 Å
AuthorsSchuller, D.J. / Poulos, T.L.
CitationJournal: Structure / Year: 1996
Title: The crystal structure of peanut peroxidase.
Authors: Schuller, D.J. / Ban, N. / Huystee, R.B. / McPherson, A. / Poulos, T.L.
History
DepositionJan 23, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_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_asym_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 2.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
B: PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0289
Polymers62,4142
Non-polymers1,6147
Water1,78399
1
B: PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1255
Polymers31,2071
Non-polymers9184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9034
Polymers31,2071
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.100, 97.200, 146.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.43899, 0.64242, -0.62816), (0.65757, 0.24671, 0.71185), (0.61228, -0.72556, -0.31413)
Vector: 19.31394, -23.03639, 48.73469)

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Components

#1: Protein PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME / PNP


Mass: 31206.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CULTURED PEANUT CELLS / Source: (natural) Arachis hypogaea (peanut) / Cellular location: SECRETED, EXTRACELLULAR / References: UniProt: P22195, peroxidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE CYS A 44, CYS A 49, CYS B 44, CYS B 49 ARE LOOP RESIDUES INVOLVED IN BINDING DISTAL CALCIUM. ...RESIDUE CYS A 44, CYS A 49, CYS B 44, CYS B 49 ARE LOOP RESIDUES INVOLVED IN BINDING DISTAL CALCIUM. RESIDUES CYS A 176, CYS A 201, CYS B 176, CYS B 201 DEMARCATE F' AND F" HELICES UNIQUE TO CLASS III PEROXIDASES.
Has protein modificationY
Sequence detailsTHE SIDE CHAIN OF RESIDUE 1 IN EACH CHAIN IS POORLY RESOLVED; IT IS MODELED AS PCA BASED ON ...THE SIDE CHAIN OF RESIDUE 1 IN EACH CHAIN IS POORLY RESOLVED; IT IS MODELED AS PCA BASED ON BIOCHEMICAL RESULTS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG40001reservoir
215 mg/mlenzyme solution1drop
30.35 Msodium phosphate1drop
412 %PEG40001drop
535 %n-octyl-beta-D-glucoside1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 1, 1991
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 19674 / % possible obs: 86.1 % / Observed criterion σ(I): 0 / Redundancy: 2.85 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
% possible obs: 86 % / Num. measured all: 56127
Reflection shell
*PLUS
Highest resolution: 2.56 Å / Lowest resolution: 2.68 Å / % possible obs: 41 %

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Processing

Software
NameVersionClassification
HOWARDdata collection
NIELSENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLOR3.1phasing
RefinementResolution: 2.56→10 Å / σ(F): 0
Details: RESIDUES SER A 277 AND SER B 277 HAVE RAMACHANDRAN ANGLES IN THE GENEROUSLY ALLOWED REGION.
RfactorNum. reflection% reflection
Rfree0.262 -10 %
Rwork0.199 --
obs0.199 19414 85.9 %
Displacement parametersBiso mean: 12.6 Å2
Refinement stepCycle: LAST / Resolution: 2.56→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 104 99 4579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.418
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.61
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.408
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d / Dev ideal: 20.619

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