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- PDB-5jhz: Crystal Structure of Fungal MagKatG2 at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 5jhz
TitleCrystal Structure of Fungal MagKatG2 at pH 7.0
ComponentsCatalase-peroxidase 2
KeywordsOXIDOREDUCTASE
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
PROTOPORPHYRIN IX CONTAINING FE / Catalase-peroxidase 2
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGasselhuber, B. / Obinger, C. / Carpena, X.
CitationJournal: Biochemistry / Year: 2016
Title: Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase.
Authors: Gasselhuber, B. / Graf, M.M. / Jakopitsch, C. / Zamocky, M. / Nicolussi, A. / Furtmuller, P.G. / Oostenbrink, C. / Carpena, X. / Obinger, C.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Feb 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 1.3Jan 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 1.4Oct 23, 2024Group: Structure summary / Category: 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: Catalase-peroxidase 2
B: Catalase-peroxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,1534
Polymers166,9202
Non-polymers1,2332
Water30,6441701
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-84 kcal/mol
Surface area50440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.200, 109.380, 133.370
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus)
Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: KATG2, CPXB, MagKatG2, MGG_09834 / Production host: Escherichia coli (E. coli) / References: UniProt: A4QUT2, catalase-peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1701 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 15% PEG4000, 0.1 M sodium acetate, pH 4.6 (+ pH 7 phosphate soaking)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9729 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 161673 / % possible obs: 97.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.075 / Rsym value: 0.066 / Net I/σ(I): 14.6
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6

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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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.526 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18643 8122 5 %RANDOM
Rwork0.1556 ---
obs0.15713 153550 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.969 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å2-0 Å2-0 Å2
2---1.51 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11290 0 86 1701 13077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911802
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210910
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9516088
X-RAY DIFFRACTIONr_angle_other_deg0.824325097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68751516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19224.567554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.727151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5141572
X-RAY DIFFRACTIONr_chiral_restr0.090.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113833
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022805
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 581 -
Rwork0.21 11090 -
obs--96.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40880.3553-0.00180.7794-0.10510.21880.01340.01850.06040.05850.00930.0783-0.0325-0.0093-0.02280.01780.01050.01440.14640.00060.132225.90711.371-16.542
20.2253-0.01360.04640.43170.10310.4935-0.00530.0095-0.0166-0.02230.0048-0.0172-0.00590.03070.00060.00170.0073-0.00050.15280.00030.130736.436-26.103-5.375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 1500
2X-RAY DIFFRACTION2B51 - 1500

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