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- PDB-1atj: RECOMBINANT HORSERADISH PEROXIDASE C1A -

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Basic information

Entry
Database: PDB / ID: 1atj
TitleRECOMBINANT HORSERADISH PEROXIDASE C1A
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE / GLYCOPROTEIN
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
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesArmoracia rusticana (horseradish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L.
Citation
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.
#1: 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
DepositionAug 14, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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.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.pdbx_dist_value / _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 / _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: PEROXIDASE C1A
B: PEROXIDASE C1A
C: PEROXIDASE C1A
D: PEROXIDASE C1A
E: PEROXIDASE C1A
F: PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,66224
Polymers202,4826
Non-polymers4,18018
Water15,997888
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.170, 159.170, 114.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.451496, -0.892119, -0.01658), (-0.892259, -0.451516, -0.002732), (-0.005049, 0.016027, -0.999859)-0.1471, 88.1838, 75.1509
2given(-0.472728, 0.8812, 0.00372), (-0.874198, -0.468432, -0.127861), (-0.110929, -0.063695, 0.991785)-78.0095, 47.2749, -36.4426
3given(0.533996, 0.838609, 0.107624), (0.839258, -0.541173, 0.052705), (0.102442, 0.06218, -0.992794)-78.9675, 136.6891, 55.4471
4given(-0.497461, -0.86403, -0.077363), (0.864233, -0.501336, 0.041979), (-0.075056, -0.045977, 0.996119)2.3691, 89.9137, -18.0552
5given(-0.493473, 0.869745, -0.005271), (-0.869761, -0.493466, 0.002503), (-0.000424, 0.00582, 0.999983)-79.2534, 45.1891, 18.7727

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Components

#1: Protein
PEROXIDASE C1A / HORSERADISH PEROXIDASE C1A / HRP C


Mass: 33746.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Armoracia rusticana (horseradish) / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39 %
Crystal growpH: 6.5
Details: 16% (W/V) PEG 4000, 0.2 M ZINC ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5
Crystal grow
*PLUS
Method: vapor diffusion / Details: Braithwaite, A., (1976) J. Mol. Biol., 106, 229.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5-1 %protein1drop
32.61 Mmagnesium sulphate1reservoir
2Tris1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 73216 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07
Reflection shellResolution: 2.15→2.9 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.4 / Rsym value: 0.4 / % possible all: 65.4
Reflection
*PLUS
Num. measured all: 142833
Reflection shell
*PLUS
Lowest resolution: 2.19 Å / % possible obs: 65.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SCH

1sch


Resolution: 2.15→100 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 7526 10 %RANDOM
Rwork0.222 ---
obs0.222 74993 83.7 %-
Displacement parametersBiso mean: 24.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.27 Å
Luzzati d res low-100 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.15→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 49 450 3421
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.391.5
X-RAY DIFFRACTIONx_mcangle_it2.222
X-RAY DIFFRACTIONx_scbond_it2.842
X-RAY DIFFRACTIONx_scangle_it4.342.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.15→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.333 611 10 %
Rwork0.306 5481 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.IONTOPH19.ION
X-RAY DIFFRACTION3MYPARAM.HEMEMYTOPH.HEME
X-RAY DIFFRACTION4MYPARAM.MGMYTOPH.MG
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81

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