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- PDB-5ala: Structure of Leishmania major peroxidase D211R mutant (low res) -

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Basic information

Entry
Database: PDB / ID: 5ala
TitleStructure of Leishmania major peroxidase D211R mutant (low 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: 2.73 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 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ASCORBATE PEROXIDASE
B: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6257
Polymers61,2742
Non-polymers1,3515
Water1,44180
1
A: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3324
Polymers30,6371
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2923
Polymers30,6371
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.880, 79.170, 179.190
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 / / CYTOCHROME C PEROXIDASE


Mass: 30636.830 Da / Num. of mol.: 2 / 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, L-ascorbate peroxidase, cytochrome-c 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.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.67 Å3/Da / Density % sol: 53.92 % / 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: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 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: 2.73→47.69 Å / Num. obs: 18116 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Biso Wilson estimate: 67.63 Å2 / Rmerge(I) obs: 0.85 / Net I/σ(I): 18.5
Reflection shellResolution: 2.73→2.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

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

3riv


Resolution: 2.73→40.837 Å / SU ML: 0.44 / σ(F): 0.03 / Phase error: 34.24 / Stereochemistry target values: ML
Details: REFINED USING GROUP B-FACTOR AND NCS FOR 2.73A RESOLUTION. RESIDUES 301-303 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2823 1701 5.1 %
Rwork0.2092 --
obs0.2127 18041 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.8 Å2
Refinement stepCycle: LAST / Resolution: 2.73→40.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4260 0 89 80 4429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164480
X-RAY DIFFRACTIONf_angle_d1.2776082
X-RAY DIFFRACTIONf_dihedral_angle_d15.1311654
X-RAY DIFFRACTIONf_chiral_restr0.05616
X-RAY DIFFRACTIONf_plane_restr0.007784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.81030.47421220.39732653X-RAY DIFFRACTION100
2.8103-2.9010.40961480.35712639X-RAY DIFFRACTION100
2.901-3.00470.34851640.3212636X-RAY DIFFRACTION100
3.0047-3.12490.37161210.29482647X-RAY DIFFRACTION100
3.1249-3.26710.35661580.2712674X-RAY DIFFRACTION100
3.2671-3.43930.31221580.24292596X-RAY DIFFRACTION100
3.4393-3.65460.2731270.2122639X-RAY DIFFRACTION100
3.6546-3.93660.2211650.18532637X-RAY DIFFRACTION100
3.9366-4.33240.21631520.16032633X-RAY DIFFRACTION100
4.3324-4.95830.21021340.15932646X-RAY DIFFRACTION100
4.9583-6.24340.30631450.20192638X-RAY DIFFRACTION100
6.2434-40.84150.29971070.18372686X-RAY DIFFRACTION100
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)
11.1479-0.5818-0.03943.9664-1.35094.3369-0.06350.31630.0215-0.84780.0087-0.11840.39790.1110.05140.4696-0.0691-0.13090.2991-0.0010.32422.851825.0756210.2917
21.70110.32250.42231.9629-0.01682.8886-0.359-0.2810.1824-0.61480.021-0.0666-0.50090.0381-0.03610.8497-0.0714-0.05380.1141-0.070.226217.249-12.0476194.4919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 34:300)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 34:300)

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