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- PDB-3e2n: Engineering ascorbate peroxidase activity into cytochrome c peroxidase -

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Basic information

Entry
Database: PDB / ID: 3e2n
TitleEngineering ascorbate peroxidase activity into cytochrome c peroxidase
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Cytochrome c peroxidase (CCP) / Ascorbate peroxidase (APX)
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / cytochrome-c peroxidase / cytochrome-c peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress ...L-ascorbate peroxidase / L-ascorbate peroxidase activity / cytochrome-c peroxidase / cytochrome-c peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / 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 ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / 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 / Cytochrome c peroxidase, mitochondrial / L-ascorbate peroxidase, cytosolic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Pisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPoulos, T.L. / Meharenna, Y.T. / Oertel, P.
CitationJournal: Biochemistry / Year: 2008
Title: Engineering ascorbate peroxidase activity into cytochrome c peroxidase.
Authors: Meharenna, Y.T. / Oertel, P. / Bhaskar, B. / Poulos, T.L.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2192
Polymers32,6021
Non-polymers6161
Water10,611589
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.783, 74.494, 50.948
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 Cytochrome c peroxidase / CCP


Mass: 32602.473 Da / Num. of mol.: 1 / Fragment: UNP residues 68-361, see remark 999 / Mutation: N251R, W258F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Pisum sativum (garden pea)
Gene: CCP1, CCP, CPO, YKR066C, APX1,APPX1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P00431, UniProt: P48534
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 97-109 (LREDDEYDNYIGY) OF THE WILD-TYPE CYTOCHROME C PEROXIDASE (CCP) ARE REPLACED WITH ...RESIDUES 97-109 (LREDDEYDNYIGY) OF THE WILD-TYPE CYTOCHROME C PEROXIDASE (CCP) ARE REPLACED WITH RESIDUES 27-32 (IAEKKC) OF THE ASCORBATE PEROXIDASE (APX).

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 298 K / pH: 6
Details: 22% 2-methyl-2,4-pentanediol (MPD), 0.05M Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 92280 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.05 / Net I/σ(I): 11
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.55 / % possible all: 93.1

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Processing

Software
NameVersionClassification
SHELXL-97refinement
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
SHELXDphasing
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZBY

1zby


Resolution: 1.3→10 Å / Num. parameters: 18483 / Num. restraintsaints: 21282 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rwork0.1812 ---
all0.1812 92099 --
obs0.1812 92099 91.9 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2867.5
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 43 589 2910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0257
X-RAY DIFFRACTIONs_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.3→1.35 Å

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