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- PDB-5whs: Crystal structure of the catalase-peroxidase from Neurospora cras... -

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Basic information

Entry
Database: PDB / ID: 5whs
TitleCrystal structure of the catalase-peroxidase from Neurospora crassa at 2.6 A
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase-peroxidase / Neurospora crassa / heme / hydrogen peroxide
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / 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
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDiaz-Vilchis, A. / Vega-Garcia, V. / Rudino-Pinera, E. / Hansberg, W.
Funding support Mexico, 1items
OrganizationGrant numberCountry
PAPIIT-UNAMIN208717 Mexico
CitationJournal: Arch. Biochem. Biophys. / Year: 2018
Title: Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase.
Authors: Vega-Garcia, V. / Diaz-Vilchis, A. / Saucedo-Vazquez, J.P. / Solano-Peralta, A. / Rudino-Pinera, E. / Hansberg, W.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,6554
Polymers170,4222
Non-polymers1,2332
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-87 kcal/mol
Surface area50370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.810, 142.350, 183.110
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 / CP / Catalase-2 / Peroxidase/catalase


Mass: 85211.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: katG, cat-2, NCU05770 / Production host: Escherichia coli M15 (bacteria) / Strain (production host): M15/pREP4 / References: UniProt: Q8X182, 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.: 682 / 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: 2.87 Å3/Da / Density % sol: 57.12 % / Description: irregular brown crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 9% PEG 8,000, 225 mM magnesium chloride and 100 mM Tris-HCl, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 30, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→112.38 Å / Num. obs: 58654 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5I05

5i05


Resolution: 2.6→112.38 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.88 / SU B: 12.777 / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.644 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2000 3.4 %RANDOM
Rwork0.209 ---
obs0.21 56550 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→112.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11196 0 86 682 11964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01911608
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210726
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.95615790
X-RAY DIFFRACTIONr_angle_other_deg1.357324688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.31151418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10623.806536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.105151824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6731574
X-RAY DIFFRACTIONr_chiral_restr0.1490.21642
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113244
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022754
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: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 147 -
Rwork0.305 4148 -
obs--99.98 %

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