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- PDB-5al9: Structure of Leishmania major peroxidase D211R mutant (high res) -

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Basic information

Entry
Database: PDB / ID: 5al9
TitleStructure of Leishmania major peroxidase D211R mutant (high res)
ComponentsASCORBATE PEROXIDASE
KeywordsOXIDOREDUCTASE
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: 1.37 Å
AuthorsChreifi, G. / Hollingsworth, S.A. / Li, H. / Tripathi, S. / Arce, A.P. / Magana-Garcia, H.I. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2015
Title: Enzymatic Mechanism of Leishmania major Peroxidase and the Critical Role of Specific Ionic Interactions.
Authors: Chreifi, G. / Hollingsworth, S.A. / Li, H. / Tripathi, S. / Arce, A.P. / Magana-Garcia, H.I. / Poulos, T.L.
History
DepositionMar 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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_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_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_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_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_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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3324
Polymers30,6371
Non-polymers6963
Water4,990277
1
A: ASCORBATE PEROXIDASE
hetero molecules

A: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6658
Polymers61,2742
Non-polymers1,3916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4540 Å2
ΔGint-59.7 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.439, 57.860, 36.620
Angle α, β, γ (deg.)90.00, 97.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ASCORBATE PEROXIDASE / CYTOCHROME C PEROXIDASE


Mass: 30636.830 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN, RESIDUES 35-303 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q3K2, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THERE IS A POSITIVE DENSITY CONSISTENT WITH A DIATOMIC ...PROTOPORPHYRIN IX CONTAINING FE (HEM): THERE IS A POSITIVE DENSITY CONSISTENT WITH A DIATOMIC MOLECULE COVALENTLY LINKED TO THE HEME MESO- CARBON CHB

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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: 2.45 Å3/Da / Density % sol: 49.87 % / Description: NONE
Crystal growpH: 6.5
Details: 10% PEG MME 5000, 0.1M MES:NAOH PH 6.5, 5% DMSO, 7.5 MM PRASEODIMIUM(III) ACETATE HYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→53.54 Å / Num. obs: 61602 / % possible obs: 98.1 % / Observed criterion σ(I): 6 / Redundancy: 2.5 % / Biso Wilson estimate: 12.32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 1.37→1.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.5 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RIV

3riv


Resolution: 1.37→36.511 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 20.53 / Stereochemistry target values: ML / Details: RESIDUES 301-303 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2037 6049 5.1 %
Rwork0.1848 --
obs0.1858 60860 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.35 Å2
Refinement stepCycle: LAST / Resolution: 1.37→36.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 45 277 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242257
X-RAY DIFFRACTIONf_angle_d1.1183077
X-RAY DIFFRACTIONf_dihedral_angle_d13.82834
X-RAY DIFFRACTIONf_chiral_restr0.074309
X-RAY DIFFRACTIONf_plane_restr0.006394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.38560.34081860.32313647X-RAY DIFFRACTION97
1.3856-1.40190.26382580.30473816X-RAY DIFFRACTION99
1.4019-1.4190.32742220.28253783X-RAY DIFFRACTION99
1.419-1.43690.27381840.27863779X-RAY DIFFRACTION99
1.4369-1.45580.27822030.2563876X-RAY DIFFRACTION99
1.4558-1.47580.2352360.2483766X-RAY DIFFRACTION99
1.4758-1.49690.2911770.24793771X-RAY DIFFRACTION99
1.4969-1.51920.25662250.23563826X-RAY DIFFRACTION98
1.5192-1.54290.26382070.23433722X-RAY DIFFRACTION99
1.5429-1.56820.27371960.22763863X-RAY DIFFRACTION99
1.5682-1.59530.21682030.21393878X-RAY DIFFRACTION99
1.5953-1.62430.20551980.21173734X-RAY DIFFRACTION99
1.6243-1.65550.21662000.20313896X-RAY DIFFRACTION99
1.6555-1.68930.21161760.20173744X-RAY DIFFRACTION99
1.6893-1.72610.21272070.19683860X-RAY DIFFRACTION99
1.7261-1.76620.2021960.18933800X-RAY DIFFRACTION99
1.7662-1.81040.21852250.1893838X-RAY DIFFRACTION99
1.8104-1.85930.20771970.18323787X-RAY DIFFRACTION99
1.8593-1.9140.22312010.17883816X-RAY DIFFRACTION99
1.914-1.97580.19521890.16573825X-RAY DIFFRACTION99
1.9758-2.04640.17352150.16283778X-RAY DIFFRACTION99
2.0464-2.12840.18311960.16043828X-RAY DIFFRACTION98
2.1284-2.22520.18112000.16813771X-RAY DIFFRACTION98
2.2252-2.34250.2142070.16623775X-RAY DIFFRACTION98
2.3425-2.48920.20631870.1693780X-RAY DIFFRACTION98
2.4892-2.68140.23792040.17163755X-RAY DIFFRACTION98
2.6814-2.95110.20272010.16813786X-RAY DIFFRACTION98
2.9511-3.37790.18851850.17053758X-RAY DIFFRACTION97
3.3779-4.25470.15631940.15293788X-RAY DIFFRACTION98
4.2547-36.52350.16241740.18553361X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -23.5726 Å / Origin y: -9.5031 Å / Origin z: 15.981 Å
111213212223313233
T0.0659 Å20.0199 Å2-0.0023 Å2-0.061 Å2-0.0076 Å2--0.0534 Å2
L1.4382 °20.6018 °2-0.0037 °2-1.0926 °2-0.0227 °2--0.7584 °2
S-0.0337 Å °0.0022 Å °-0.0291 Å °-0.0204 Å °0.0345 Å °-0.0017 Å °0.0381 Å °0.0651 Å °-0.0009 Å °
Refinement TLS groupSelection details: ALL

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