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- PDB-1h5i: X-ray induced reduction of horseradish peroxidase C1A Compound II... -

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Basic information

Entry
Database: PDB / ID: 1h5i
TitleX-ray induced reduction of horseradish peroxidase C1A Compound III (56-67% dose)
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE / HORSERADISH / COMPOUND III / OXYPEROXIDASE / X-RAY INDUCED REDUCTION
Function / homology
Function and homology information


lactoperoxidase activity / peroxidase / 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 / HYDROGEN PEROXIDE / Peroxidase C1A
Similarity search - Component
Biological speciesARMORACIA RUSTICANA (horseradish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 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 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)34,8409
Polymers33,9481
Non-polymers8928
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.318, 67.392, 117.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 401 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


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: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 7

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Description: X-RAY EXPOSURE CORRESPONDS TO 56-67% X-RAY DOSE (SEE JRNL). AN X-RAY DOSE OF 0-100% REPRESENTS THE DOSE REQUIRED FOR THE COLLECTION OF A COMPLETE DATA SET FROM ONE CRYSTAL. STARTING ...Description: X-RAY EXPOSURE CORRESPONDS TO 56-67% X-RAY DOSE (SEE JRNL). AN X-RAY DOSE OF 0-100% REPRESENTS THE DOSE REQUIRED FOR THE COLLECTION OF A COMPLETE DATA SET FROM ONE CRYSTAL. 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 AND 0.1 M CACODYLATE BUFFER, PH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
20.2 Mcalcium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH6.5
47.3 mg/mlprotein1drop
50.1 Mcacodylate1droppH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→33.9 Å / Num. obs: 38857 / % possible obs: 90.2 % / Redundancy: 2.45 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.6 / % possible all: 77.3
Reflection
*PLUS
Num. measured all: 95385

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.6→33.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1369233.3 / 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: 24,151,161,188,219,240,249, 264,286,732, AND HOH 297
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1938 5 %RANDOM
Rwork0.191 ---
obs0.191 38857 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1524 Å2 / ksol: 0.398757 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--2.08 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 57 393 2819
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 278 4.9 %
Rwork0.211 5444 -
obs--80.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION5ION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
LS refinement shell
*PLUS
Rfactor obs: 0.211

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