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- PDB-6atj: RECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID -

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Basic information

Entry
Database: PDB / ID: 6atj
TitleRECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE / REDUCING SUBSTRATE
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / vacuole / 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
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesArmoracia rusticana (horseradish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHenriksen, A. / Smith, A.T. / Gajhede, M.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates.
Authors: Henriksen, A. / Smith, A.T. / Gajhede, M.
#1: Journal: Biochemistry / Year: 1998
Title: Structural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography.
Authors: Henriksen, A. / Schuller, D.J. / Meno, K. / Welinder, K.G. / Smith, A.T. / Gajhede, M.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of horseradish peroxidase C at 2.15 A resolution.
Authors: Gajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallization and preliminary X-ray studies of recombinant horseradish peroxidase.
Authors: Henriksen, A. / Gajhede, M. / Baker, P. / Smith, A.T. / Burke, J.F.
History
DepositionApr 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8395
Polymers33,9481
Non-polymers8914
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.297, 67.272, 117.646
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 C1A / HORSERADISH PEROXIDASE C1A / HRP C


Mass: 33948.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Armoracia rusticana (horseradish) / Description: SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SWS ENTRY INCLUDES N-TERM AND C-TERM SIGNAL PEPTIDES.

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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: 2.35 Å3/Da / Density % sol: 47.5 %
Crystal growpH: 6.5
Details: 16% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)PEG80001reservoir
20.2 M1reservoirCa(CH3COO)2
30.1 Mcacodylate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. obs: 21778 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 2.9 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.208 / % possible all: 96
Reflection
*PLUS
% possible obs: 97.2 % / Num. measured all: 108409
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

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

1atj


Resolution: 2→29 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 344924.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1045 4.9 %RANDOM
Rwork0.166 ---
obs-21281 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---2.16 Å20 Å2
3---2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 87 399 2954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
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: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 161 4.8 %
Rwork0.178 3202 -
obs--91.9 %
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 21751
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37

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