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- PDB-1w4y: Ferrous horseradish peroxidase C1A in complex with carbon monoxide -

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Basic information

Entry
Database: PDB / ID: 1w4y
TitleFerrous horseradish peroxidase C1A in complex with carbon monoxide
ComponentsHORSERADISH PEROXIDASE C1A
KeywordsOXIDOREDUCTASE / CARBON MONOXIDE / CALCIUM / FERROUS STATE / GLYCOPROTEIN / HEME / HORSERADISH / IRON / MULTIGENE FAMILY / PEROXIDASE / PYRROLIDONE CARBOXYLIC 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesARMORACIA RUSTICANA (horseradish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCarlsson, G.H. / Nicholls, P. / Svistunenko, D. / Berglund, G.I. / Hajdu, J.
Citation
Journal: Biochemistry / Year: 2005
Title: Complexes of Horseradish Peroxidase with Formate, Acetate, and Carbon Monoxide
Authors: Carlsson, G.H. / Nicholls, P. / Svistunenko, D. / Berglund, G.I. / Hajdu, J.
#1: 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.
#2: 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
DepositionAug 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: 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
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Nov 27, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HORSERADISH PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3775
Polymers35,6521
Non-polymers7254
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.430, 67.563, 117.192
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 HORSERADISH PEROXIDASE C1A


Mass: 35652.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CARBON MONOXIDE BOUND TO THE FERROUS IRON / Source: (gene. exp.) ARMORACIA RUSTICANA (horseradish) / 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG8000, 0.2 M CA-ACETATE, 0.1 M NA-CACODYLATE PH 6.5, FERULIC ACID AS ADDITIVE, HANGING DROP, STREAK SEEDING, 4DEGC

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.089
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2003 / Details: SI(III)
RadiationMonochromator: MULTIPOLE WIGGLER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.089 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 41633 / % possible obs: 90.4 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.3
Reflection shellResolution: 1.57→1.61 Å / Rmerge(I) obs: 0.3 / % possible all: 86.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H58

1h58


Resolution: 1.6→25.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1352591.14 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1949 5 %RANDOM
Rwork0.199 ---
obs0.199 39205 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2791 Å2 / ksol: 0.371891 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--2.44 Å20 Å2
3----1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→25.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 47 341 2757
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
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
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_it1.352
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.092.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 278 4.6 %
Rwork0.234 5767 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3HEM_FE2.PARHEM_FE2.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMCO2.TOP
X-RAY DIFFRACTION5CO2.PARION.TOP

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