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- PDB-2atj: RECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID -

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Basic information

Entry
Database: PDB / ID: 2atj
TitleRECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE
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
BENZHYDROXAMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesArmoracia rusticana (horseradish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHenriksen, A. / Schuller, D.J. / Gajhede, M.
Citation
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.
#1: 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.
#2: 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 19, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65210
Polymers67,9852
Non-polymers1,6688
Water6,521362
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A: PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8265
Polymers33,9921
Non-polymers8344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8265
Polymers33,9921
Non-polymers8344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.920, 62.250, 77.990
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.0063, 0.0026), (0.0063, -1, 0.0072), (0.0026, 0.0072, 1)
Vector: 18.0698, 29.6212, 0.0409)

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Components

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


Mass: 33992.262 Da / Num. of mol.: 2
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.: 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: Chemical ChemComp-BHO / BENZHYDROXAMIC ACID


Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 283 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.35 mMBHA1drop
26.0 mg/mlHRPC1drop
31.0 M1reservoirNH42HPO4
40.1 Mcacodylate 1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 46595 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2→2.1 Å / % possible all: 92.8
Reflection
*PLUS
Num. measured all: 144839
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.3

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Processing

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

1sch


Resolution: 2→30 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: A BULK SOLVENT MODEL USED. THE STRUCTURE WAS REFINED USING STRICT NON- CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS.
RfactorNum. reflection% reflection
Rfree0.198 4746 10.2 %
Rwork0.176 --
obs0.176 46515 98.5 %
Displacement parametersBiso mean: 14.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 55 181 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.92
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.361.5
X-RAY DIFFRACTIONx_mcangle_it2.12
X-RAY DIFFRACTIONx_scbond_it2.752
X-RAY DIFFRACTIONx_scangle_it3.962.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.245 555 10.3 %
Rwork0.217 4829 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ELEMENTS.PARAMHEME.TOPH, BHA.PARAM
X-RAY DIFFRACTION2PROTEIN.PARAMSOL.TOPH
X-RAY DIFFRACTION3HEME.PARAM, BHA.PARAMPROTEIN.TOPH
X-RAY DIFFRACTION4SOL.PARAMELEMENTS.TOPH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28.6 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.09
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.92

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