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- PDB-3riv: The Crystal Structure of Leishmania major Peroxidase -

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Basic information

Entry
Database: PDB / ID: 3riv
TitleThe Crystal Structure of Leishmania major Peroxidase
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / Alpha Helical Bundle / Heme Peroxidase
Function / homology
Function and homology information


iodide peroxidase activity / L-ascorbate oxidase activity / L-ascorbate peroxidase activity / stabilization of membrane potential / cytochrome-c peroxidase / cytochrome-c peroxidase activity / cytochrome-c oxidase activity / calcium ion homeostasis / reactive oxygen species metabolic process / response to reactive oxygen species ...iodide peroxidase activity / L-ascorbate oxidase activity / L-ascorbate peroxidase activity / stabilization of membrane potential / cytochrome-c peroxidase / cytochrome-c peroxidase activity / cytochrome-c oxidase activity / calcium ion homeostasis / reactive oxygen species metabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / 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 / Peroxidase; domain 1 / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Haem peroxidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsJasion, V.S. / Li, H. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Leishmania major Peroxidase and Characterization of the Compound I Tryptophan Radical.
Authors: Jasion, V.S. / Polanco, J.A. / Meharenna, Y.T. / Li, H. / Poulos, T.L.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ascorbate peroxidase
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7838
Polymers61,3922
Non-polymers1,3916
Water7,981443
1
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3914
Polymers30,6961
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3914
Polymers30,6961
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.601, 77.187, 156.022
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 Ascorbate peroxidase /


Mass: 30695.830 Da / Num. of mol.: 2 / Fragment: C-terminal catalytic domain (UNP residues 35-303)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: APX, LMJF_34_0070 / Plasmid: pPAL7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q3K2, L-ascorbate peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, potassium chloride, glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.76→37.464 Å / Num. obs: 56061 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 33.22
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.01 / Num. unique all: 2779 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
DMmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→37.464 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.327 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20876 2835 5.1 %RANDOM
Rwork0.16899 ---
obs0.17097 53057 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.465 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2--0.35 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.76→37.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 90 443 4775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224451
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.0246047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5975530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99223.942208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8915748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4611528
X-RAY DIFFRACTIONr_chiral_restr0.0960.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213438
X-RAY DIFFRACTIONr_mcbond_it0.8231.52653
X-RAY DIFFRACTIONr_mcangle_it1.54724258
X-RAY DIFFRACTIONr_scbond_it2.68531798
X-RAY DIFFRACTIONr_scangle_it4.3484.51789
LS refinement shellResolution: 1.765→1.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 192 -
Rwork0.221 3662 -
obs--93.86 %

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