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- PDB-4e08: Crystal structure of Drosophila melanogaster DJ-1beta -

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Basic information

Entry
Database: PDB / ID: 400000000
TitleCrystal structure of Drosophila melanogaster DJ-1beta
ComponentsDJ-1 beta
KeywordsMOTOR PROTEIN / flavodoxin-like fold / stress response
Function / homology
Function and homology information


regulation of mitochondrial ATP synthesis coupled electron transport / regulation of neuromuscular synaptic transmission / negative regulation of developmental growth / larval locomotory behavior / : / protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / regulation of hydrogen peroxide metabolic process ...regulation of mitochondrial ATP synthesis coupled electron transport / regulation of neuromuscular synaptic transmission / negative regulation of developmental growth / larval locomotory behavior / : / protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / regulation of hydrogen peroxide metabolic process / adult locomotory behavior / regulation of synaptic plasticity / cellular response to reactive oxygen species / response to oxidative stress / mitochondrion / nucleus / cytosol
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, J. / Prahlad, J. / Wilson, M.A.
CitationJournal: Biochemistry / Year: 2012
Title: Conservation of Oxidative Protein Stabilization in an Insect Homologue of Parkinsonism-Associated Protein DJ-1.
Authors: Lin, J. / Prahlad, J. / Wilson, M.A.
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Jun 20, 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 / 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 / _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: DJ-1 beta
B: DJ-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1993
Polymers39,1032
Non-polymers961
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-29 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.520, 52.520, 227.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21B-201-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.489001, -0.867377, 0.092386), (-0.867238, 0.472062, -0.158291), (0.093687, -0.157525, -0.983061)-6.7118, -0.44819, 32.18166

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Components

#1: Protein DJ-1 beta / Dj-1beta / GH09983p


Mass: 19551.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1349, dj-1 beta, dj-1-beta, dj-1beta, Dmel_CG1349 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VA37
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH=4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2010 / Details: K-B PAIR OF BIOMORPH MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→76 Å / Num. all: 25116 / Num. obs: 25116 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.098 / Net I/σ(I): 21.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2112 / Rsym value: 0.587 / % possible all: 83.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIXmodel building
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OR3

2or3


Resolution: 2→75.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.18 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24559 1267 5.1 %RANDOM
Rwork0.19318 ---
all0.19579 23814 --
obs0.19579 23814 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.734 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.9 Å2-0 Å2
2--1.79 Å2-0 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2→75.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 5 278 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222718
X-RAY DIFFRACTIONr_angle_refined_deg1.5032.0013677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14425.68288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53615475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0471510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211964
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 75 -
Rwork0.296 1314 -
obs-1314 81.8 %
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)
11.948-0.6136-0.12521.3286-0.08182.19260.2126-0.09770.2380.1411-0.0977-0.0337-0.2860.2388-0.11490.0945-0.05490.0450.0461-0.02570.034815.6331-15.149528.5415
21.4841-0.36060.32182.00040.13842.52940.16180.2889-0.0361-0.1106-0.11090.12920.0736-0.0463-0.05090.04060.0596-0.01610.1036-0.01690.0121.4812-25.7487.9722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 186
2X-RAY DIFFRACTION2B1 - 186

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