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- PDB-3riw: The Crystal Structure of Leishmania major Peroxidase mutant C197T -

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Basic information

Entry
Database: PDB / ID: 3riw
TitleThe Crystal Structure of Leishmania major Peroxidase mutant C197T
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 / MOLECULAR REPLACEMENT / Resolution: 2.37 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,7798
Polymers61,3882
Non-polymers1,3916
Water2,144119
1
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3894
Polymers30,6941
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3894
Polymers30,6941
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.819, 77.766, 160.580
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: 30693.791 Da / Num. of mol.: 2 / Fragment: C-terminal catalytic domain (UNP residues 35-303) / Mutation: C197T
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, potassium chloride, calcium chloride, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.369→35.426 Å / Num. obs: 23951 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 17.15
Reflection shellResolution: 2.38→2.42 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.08 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→35.426 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.232 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24056 1215 5.1 %RANDOM
Rwork0.17832 ---
obs0.1814 22558 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.754 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--0.47 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.37→35.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 90 119 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224466
X-RAY DIFFRACTIONr_angle_refined_deg1.462.0246070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67623.942208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.631528
X-RAY DIFFRACTIONr_chiral_restr0.1080.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213450
X-RAY DIFFRACTIONr_mcbond_it0.6391.52664
X-RAY DIFFRACTIONr_mcangle_it1.324278
X-RAY DIFFRACTIONr_scbond_it2.5231802
X-RAY DIFFRACTIONr_scangle_it4.0544.51792
LS refinement shellResolution: 2.369→2.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 63 -
Rwork0.196 1476 -
obs--87.2 %
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)
11.4894-0.26480.45481.0505-0.40191.5025-0.0284-0.05430.01580.0584-0.0235-0.0494-0.12770.03330.05190.022-0.00540.01010.00910.00380.0299-18.312712.1201-27.3785
20.7627-0.1177-0.36321.2934-0.49792.1275-0.0565-0.0689-0.03290.15660.04280.02680.14770.04690.01370.05680.0074-0.00420.0544-0.0220.0261-17.921348.5785-10.8773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 305
2X-RAY DIFFRACTION2B34 - 305

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