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- PDB-1h58: STRUCTURE OF FERROUS HORSERADISH PEROXIDASE C1A -

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Basic information

Entry
Database: PDB / ID: 1h58
TitleSTRUCTURE OF FERROUS HORSERADISH PEROXIDASE C1A
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE / HORSERADISH / FERROUS STATE
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 / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesARMORACIA RUSTICANA (horseradish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsBerglund, G.I. / Carlsson, G.H. / Hajdu, J. / Smith, A.T. / Szoke, H. / Henriksen, A.
Citation
Journal: Nature / Year: 2002
Title: The Catalytic Pathway of Horseradish Peroxidase at High Resolution
Authors: Berglund, G.I. / Carlsson, G.H. / Smith, A.T. / Szoke, H. / Henriksen, A. / Hajdu, J.
#1: 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.
#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: J.Biol.Chem. / Year: 1990
Title: Expression of a Synthetic Gene for Horseradish Peroxidase C in Escherichia Coli and Folding and Activation of the Recombinant Enzyme with Ca2+ and Heme
Authors: Smith, A.T. / Santama, N. / Dacey, S. / Edwards, M. / Bray, R.C. / Thorneley, R.N. / Burke, J.F.
History
DepositionMay 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site

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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)34,7045
Polymers33,9481
Non-polymers7564
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.266, 67.091, 117.523
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


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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.1 %
Description: STARTING MODEL FOR RIGID-BODY REFINEMENT WAS PDB ENTRY 7ATJ
Crystal growpH: 6.5
Details: 20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5 THE FERROUS STATE WAS FORMED BY SOAKING THE CRYSTALS FOR 30 MINUTES IN A RESERVOIR SOLUTION SUPPLEMENTED WITH 100 ...Details: 20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5 THE FERROUS STATE WAS FORMED BY SOAKING THE CRYSTALS FOR 30 MINUTES IN A RESERVOIR SOLUTION SUPPLEMENTED WITH 100 MM SODIUM DITHIONITE AND PEG400 BEFORE FLASH FREEZING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.983
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.7→25.9 Å / Num. obs: 34886 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 6.6 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.7→25.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1391483.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SER 306 WAS THE LAST RESIDUE SEEN IN THE ELECTRON DENSITY MAP THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN DUAL CONFORMATIONS: 15,16,24,73,91,151,161,176, 203,219,240,264 297,301,303
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1775 5.1 %RANDOM
Rwork0.171 ---
obs0.171 34886 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4185 Å2 / ksol: 0.378925 e/Å3
Displacement parametersBiso mean: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--1.21 Å20 Å2
3----1.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 49 423 2841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
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_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.332
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 1.6→1.7 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.178 5 -
obs--0.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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