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- PDB-4ge0: Schizosaccharomyces pombe DJ-1 T114P mutant -

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Basic information

Entry
Database: PDB / ID: 4ge0
TitleSchizosaccharomyces pombe DJ-1 T114P mutant
ComponentsUncharacterized protein C22E12.03c
KeywordsUNKNOWN FUNCTION / DJ-1/PfpI family / Cysteine-sulfinic acid
Function / homology
Function and homology information


SUMOylation of transcription cofactors / D-lactate dehydratase / glyoxalase III activity / glyoxal metabolic process / cellular detoxification / response to oxidative stress / mitochondrion / nucleus / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMadzelan, P. / Labunska, T. / Wilson, 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
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Nov 19, 2014Group: Non-polymer description
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Sep 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_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.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.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_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)85,8238
Polymers85,6504
Non-polymers1734
Water16,718928
1
A: Uncharacterized protein C22E12.03c
B: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8873
Polymers42,8252
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-13 kcal/mol
Surface area14770 Å2
MethodPISA
2
C: Uncharacterized protein C22E12.03c
D: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9365
Polymers42,8252
Non-polymers1113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-15 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.486, 51.743, 82.749
Angle α, β, γ (deg.)89.10, 89.08, 66.86
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21412.578 Da / Num. of mol.: 4 / Mutation: T114P
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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 26% 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2012 / Details: Osmic blue confocal
RadiationMonochromator: OSMIC CONFOCAL OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→37 Å / Num. all: 113462 / Num. obs: 113462 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 5.8 / Num. unique all: 10144 / % possible all: 84.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GDH

4gdh
PDB Unreleased entry


Resolution: 1.45→36.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.189 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement used with 4 groups
RfactorNum. reflection% reflectionSelection details
Rfree0.20772 5669 5 %RANDOM
Rwork0.1787 ---
all0.18014 113457 --
obs0.18014 113457 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.35 Å20.37 Å2
2--0.25 Å20.08 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 10 928 6842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226443
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9868767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54525.118254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.549151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9991522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214902
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.527 372 -
Rwork0.512 7027 -
obs-7399 82.76 %
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)
11.0016-0.146-0.16861.27180.58082.3685-0.09410.017-0.12680.07910.03250.06410.2270.02130.06160.0349-0.01110.02780.0267-0.01550.04752.778712.3831-1.5362
20.83290.0255-0.56292.22690.37291.9547-0.009-0.15230.10150.21620.0608-0.0702-0.17560.1524-0.05180.0950.00960.00670.0597-0.01090.0382.413732.724117.2518
31.1035-0.23420.2650.8777-0.28941.50140.0298-0.0448-0.03650.0122-0.0276-0.03890.0780.0853-0.00220.0064-0.0009-0.00210.03560.01910.02483.252742.5322-23.5996
41.2902-0.3075-0.270.9743-0.07491.45970.02560.13090.0148-0.1713-0.00090.0684-0.079-0.1342-0.02470.0463-0.0011-0.00860.04960.01510.0233-12.948154.5808-42.6121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 191
2X-RAY DIFFRACTION2B2 - 191
3X-RAY DIFFRACTION3C2 - 191
4X-RAY DIFFRACTION4D2 - 191

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