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- PDB-5via: Crystal structural of Leishmania major pseudoperoxidase -

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Basic information

Entry
Database: PDB / ID: 5via
TitleCrystal structural of Leishmania major pseudoperoxidase
ComponentsPseudoperoxidase
KeywordsOXIDOREDUCTASE / heme protein / peroxidase
Function / homology
Function and homology information


response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / membrane => GO:0016020 / heme binding / metal ion binding
Similarity search - Function
Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PEROXIDASE_4 domain-containing protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.764 Å
AuthorsChreifi, G. / Dejam, D. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2017
Title: Crystal structure and functional analysis of Leishmania major pseudoperoxidase.
Authors: Chreifi, G. / Dejam, D. / Poulos, T.L.
History
DepositionApr 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6832
Polymers33,0661
Non-polymers6161
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.680, 63.680, 152.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-757-

HOH

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Components

#1: Protein Pseudoperoxidase / Uncharacterized protein


Mass: 33066.293 Da / Num. of mol.: 1 / Fragment: UNP residues 49-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_21_1567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QC30
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 mg/mL protein, 5% 2-methyl-2,4-pentanediol, 10% polyethylene glycol 6000, and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.76→48.88 Å / Num. obs: 31236 / % possible obs: 98.22 % / Redundancy: 18 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.049 / Net I/σ(I): 73.11
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 16.5 % / Num. unique obs: 3100 / CC1/2: 0.297 / % possible all: 94.03

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.764→48.875 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1522 4.86 %Random selection
Rwork0.1957 ---
obs0.1969 31200 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.764→48.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 43 181 2429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072309
X-RAY DIFFRACTIONf_angle_d1.0483149
X-RAY DIFFRACTIONf_dihedral_angle_d14.239844
X-RAY DIFFRACTIONf_chiral_restr0.065341
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.764-1.79450.42221340.40082632X-RAY DIFFRACTION95
1.7945-1.82710.37191680.37532635X-RAY DIFFRACTION94
1.8271-1.86220.34451270.3712672X-RAY DIFFRACTION95
1.8622-1.90030.33751570.34172658X-RAY DIFFRACTION95
1.9003-1.94160.382860.3312763X-RAY DIFFRACTION97
1.9416-1.98670.29361370.31082764X-RAY DIFFRACTION97
1.9867-2.03640.28621210.28172735X-RAY DIFFRACTION97
2.0364-2.09150.29971280.26432774X-RAY DIFFRACTION98
2.0915-2.1530.28841730.24282728X-RAY DIFFRACTION99
2.153-2.22250.26581610.23532756X-RAY DIFFRACTION99
2.2225-2.3020.29911460.22912788X-RAY DIFFRACTION100
2.302-2.39410.20231380.21732805X-RAY DIFFRACTION100
2.3941-2.50310.26551310.20012816X-RAY DIFFRACTION100
2.5031-2.6350.17041450.17982800X-RAY DIFFRACTION100
2.635-2.80010.23081300.18012825X-RAY DIFFRACTION100
2.8001-3.01630.19861440.17782812X-RAY DIFFRACTION100
3.0163-3.31980.23271360.17062808X-RAY DIFFRACTION100
3.3198-3.80.16071440.15662799X-RAY DIFFRACTION100
3.8-4.78690.17381650.15112787X-RAY DIFFRACTION100
4.7869-48.89410.20971470.18742798X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.8372 Å / Origin y: 41.2282 Å / Origin z: 60.1489 Å
111213212223313233
T0.1681 Å20.0055 Å2-0.0109 Å2-0.2404 Å20.0527 Å2--0.1655 Å2
L2.6912 °20.1807 °20.6496 °2-1.7126 °20.3026 °2--2.4513 °2
S-0.0276 Å °0.311 Å °0.1501 Å °-0.1645 Å °0.0506 Å °0.0278 Å °0.1125 Å °0.0848 Å °-0.0224 Å °
Refinement TLS groupSelection details: (chain A and resid 56:333)

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