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- PDB-5cjh: Crystal Structure of Eukaryotic Oxoiron MagKatG2 at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 5cjh
TitleCrystal Structure of Eukaryotic Oxoiron MagKatG2 at pH 8.5
ComponentsCatalase-peroxidase 2
KeywordsOXIDOREDUCTASE / COMPOUND I / OXOIRON CATALASE-PEROXIDASE
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / extracellular region / metal ion binding / cytosol
Similarity search - Function
Catalase-peroxidase haem / 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 ...Catalase-peroxidase haem / 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
Peroxidized Heme / HYDROXIDE ION / Catalase-peroxidase 2
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGasselhuber, B. / Obinger, C. / Fita, I. / Carpena, X.
CitationJournal: Biochemistry / Year: 2015
Title: Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation.
Authors: Gasselhuber, B. / Carpena, X. / Graf, M.M. / Pirker, K.F. / Nicolussi, A. / Sundermann, A. / Hofbauer, S. / Zamocky, M. / Furtmuller, P.G. / Jakopitsch, C. / Oostenbrink, C. / Fita, I. / Obinger, C.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Structure summary
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase-peroxidase 2
B: Catalase-peroxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,2556
Polymers166,9202
Non-polymers1,3354
Water28,3381573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-54 kcal/mol
Surface area50530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.530, 109.540, 132.150
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 Catalase-peroxidase 2 / CP 2 / Peroxidase/catalase 2


Mass: 83460.188 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus)
Gene: KATG2, CPXB, MagKatG2, MGG_09834 / Production host: Escherichia coli (E. coli) / References: UniProt: A4QUT2, catalase-peroxidase
#2: Chemical ChemComp-522 / Peroxidized Heme


Mass: 650.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O6
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1573 / 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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG4000, 0.1 M sodium acetate, pH 4.6 (+ PAA soaking + pH 8.5 soaking)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 196582 / % possible obs: 99.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.099 / Rsym value: 0.087 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UT2

3ut2


Resolution: 1.6→19.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.51 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18992 9850 5 %RANDOM
Rwork0.16472 ---
obs0.16597 186717 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.5 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11283 0 92 1573 12948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911853
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210918
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.94916172
X-RAY DIFFRACTIONr_angle_other_deg0.794325124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33251529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31824.549565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2961574
X-RAY DIFFRACTIONr_chiral_restr0.0780.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113936
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022828
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 759 -
Rwork0.259 13557 -
obs--99.31 %

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