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- PDB-4ged: Crystal Structure of the Leishmania Major Peroxidase-Cytochrome C... -

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Basic information

Entry
Database: PDB / ID: 4ged
TitleCrystal Structure of the Leishmania Major Peroxidase-Cytochrome C Complex
Components
  • Ascorbate peroxidase
  • Cytochrome c
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / ALPHA HELICAL BUNDLE / HEME PEROXIDASE / cytochrome c peroxidase / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
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 / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : ...iodide peroxidase activity / L-ascorbate oxidase activity / L-ascorbate peroxidase activity / stabilization of membrane potential / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / calcium ion homeostasis / reactive oxygen species metabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding / cytoplasm
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Cytochrome c peroxidase, mitochondrial / Cytochrome c
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsJasion, V.S. / Doukov, T. / Pineda, S.H. / Li, H. / Poulos, T.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of the Leishmania major peroxidase-cytochrome c complex.
Authors: Jasion, V.S. / Doukov, T. / Pineda, S.H. / Li, H. / Poulos, T.L.
History
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8836
Polymers42,5852
Non-polymers1,2984
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.750, 149.750, 36.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ascorbate peroxidase


Mass: 30378.531 Da / Num. of mol.: 1
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: Protein Cytochrome c / Putative cytochrome c


Mass: 12206.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_16_1310, LMJF_16_1320 / Plasmid: pBPCYC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QEN5

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Non-polymers , 5 types, 234 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32-33% pentaerythritol ethoxylate, 4% acetone, 40 mM Potassium Phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2012 / Details: Rh coated K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.83→37.4 Å / Num. all: 37026 / Num. obs: 36729 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 42.23 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.033 / Net I/σ(I): 12.4
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 0.6 / Num. unique all: 5063 / % possible all: 95.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3RIV, 4DY9

3riv

4dy9


Resolution: 1.84→31.99 Å / Cor.coef. Fo:Fc: 0.9452 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1797 5.03 %RANDOM
Rwork0.185 ---
all0.1856 37026 --
obs0.1856 35729 97.41 %-
Displacement parametersBiso mean: 59.91 Å2
Baniso -1Baniso -2Baniso -3
1--6.963 Å20 Å20 Å2
2---6.963 Å20 Å2
3---13.926 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 1.84→31.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 88 230 3227
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086178HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9111202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1696SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1120HARMONIC5
X-RAY DIFFRACTIONt_it6178HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6282SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2351 105 4.83 %
Rwork0.2155 2067 -
all0.2164 2172 -
obs-2067 97.41 %
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)
12.7160.2021-0.1951.67920.3141.2039-0.11090.0758-0.29720.0313-0.09370.2953-0.0195-0.21920.2046-0.2688-0.01220.0191-0.2446-0.09140.3242-45.108413.926117.8589
28.43091.3585-0.48944.74660.51041.9855-0.06650.135-0.2642-0.19180.2271-0.28480.1460.0799-0.1605-0.29030.0050.0309-0.3553-0.06140.4503-30.5802-9.966912.2203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 301
2X-RAY DIFFRACTION2B12 - 113

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