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- PDB-4qyt: Schizosaccharomyces pombe DJ-1 -

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Basic information

Entry
Database: PDB / ID: 4qyt
TitleSchizosaccharomyces pombe DJ-1
ComponentsUncharacterized protein C22E12.03c
KeywordsUNKNOWN FUNCTION / CYSTEINE OXIDATION
Function / homology
Function and homology information


SUMOylation of transcription cofactors / Aggrephagy / D-lactate dehydratase / glyoxalase III activity / glyoxal metabolic process / glycolate biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / cellular detoxification / response to oxidative stress / mitochondrion ...SUMOylation of transcription cofactors / Aggrephagy / D-lactate dehydratase / glyoxalase III activity / glyoxal metabolic process / glycolate biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / cellular detoxification / response to oxidative stress / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
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
Glutathione-independent glyoxalase DJ-1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsWilson, M.A.
CitationJournal: Febs J. / Year: 2012
Title: Influence of peptide dipoles and hydrogen bonds on reactive cysteine pK(a) values in fission yeast DJ-1.
Authors: Madzelan, P. / Labunska, T. / Wilson, M.A.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionAug 6, 2014ID: 4GDH
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Non-polymer description
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr2_label_seq_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: Uncharacterized protein C22E12.03c
B: Uncharacterized protein C22E12.03c
C: Uncharacterized protein C22E12.03c
D: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,28417
Polymers85,6664
Non-polymers61813
Water16,268903
1
A: Uncharacterized protein C22E12.03c
B: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0446
Polymers42,8332
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-10 kcal/mol
Surface area14640 Å2
MethodPISA
2
C: Uncharacterized protein C22E12.03c
D: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,24111
Polymers42,8332
Non-polymers4089
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-6 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.507, 51.913, 82.705
Angle α, β, γ (deg.)89.07, 88.98, 66.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein C22E12.03c / DJ-1


Mass: 21416.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC22E12.03c / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10356
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 903 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 26-32% PEG4000, 100 MM TRIS-HCL, 200 MM MAGNESIUM CHLORIDE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.78 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 1.05→87 Å / Num. all: 309118 / Num. obs: 309118 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.6
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.1 / Num. unique all: 28701 / % possible all: 90.2

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OR3

2or3


Resolution: 1.05→82.69 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.793 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13212 15603 5.1 %RANDOM
Rwork0.10961 ---
all0.11074 308911 --
obs0.11074 308911 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.18 Å2-0.26 Å2
2---0.23 Å20.16 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.05→82.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 37 903 6844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197227
X-RAY DIFFRACTIONr_bond_other_d0.0010.027028
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9879831
X-RAY DIFFRACTIONr_angle_other_deg0.958316339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28324.93284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.526151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5811525
X-RAY DIFFRACTIONr_chiral_restr0.1240.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0218292
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021547
X-RAY DIFFRACTIONr_mcbond_it1.8770.6743609
X-RAY DIFFRACTIONr_mcbond_other1.8760.6743608
X-RAY DIFFRACTIONr_mcangle_it2.1721.5234597
X-RAY DIFFRACTIONr_mcangle_other2.1721.5234598
X-RAY DIFFRACTIONr_scbond_it3.1830.8313618
X-RAY DIFFRACTIONr_scbond_other3.1830.8323619
X-RAY DIFFRACTIONr_scangle_other3.4191.7725235
X-RAY DIFFRACTIONr_long_range_B_refined3.8672.2178502
X-RAY DIFFRACTIONr_long_range_B_other3.7952.1848397
X-RAY DIFFRACTIONr_rigid_bond_restr13.033314255
X-RAY DIFFRACTIONr_sphericity_free53.4394259
X-RAY DIFFRACTIONr_sphericity_bonded13.487414706
LS refinement shellResolution: 1.049→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 1059 -
Rwork0.234 19198 -
obs-19198 86.27 %

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