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- PDB-1gw2: RECOMBINANT HORSERADISH PEROXIDASE C1A THR171SER IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1gw2
TitleRECOMBINANT HORSERADISH PEROXIDASE C1A THR171SER IN COMPLEX WITH FERULIC ACID
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE / FERULIC ACID
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
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesARMORACIA RUSTICANA (horseradish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHenriksen, A. / Meno, K. / Brissett, N. / Gajhede, M.
Citation
Journal: To be Published
Title: Hrpc Heme Crevice Architecture
Authors: Henriksen, A. / Meno, K. / Brissett, N. / Gajhede, M.
#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: 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.
#3: 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.
#4: 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
DepositionMar 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2003Provider: 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: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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 / 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_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_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

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Assembly

Deposited unit
A: PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0196
Polymers33,9341
Non-polymers1,0855
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.192, 67.000, 117.073
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: 33934.113 Da / Num. of mol.: 1 / Mutation: YES
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION: RESIDUE THR (171) SER
Sequence detailsSER A 171, SITE DIRECTED MUTATION

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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 %
Crystal growpH: 6.5
Details: 16% PEG 4000, 0.2 M CALCIUM ACETATE,0.1 M CACODYLATE BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.015
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.015 Å / Relative weight: 1
ReflectionResolution: 2.15→14.95 Å / Num. obs: 127100 / % possible obs: 92 % / Redundancy: 2.7 % / Biso Wilson estimate: 0.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 23.9 / % possible all: 90

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6ATJ

6atj


Resolution: 2.15→14.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 801182.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUES ASN 307 AND SER 308 WERE NOT SEEN IN THE ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.211 791 4.9 %RANDOM
Rwork0.165 ---
obs0.165 16279 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.836 Å2 / ksol: 0.374309 e/Å3
Displacement parametersBiso mean: 9 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--1.94 Å20 Å2
3----1.83 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2.15→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 73 389 2831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 125 4.9 %
Rwork0.161 2427 -
obs--87.6 %

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