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- PDB-4ge3: Schizosaccharomyces pombe DJ-1 T114V mutant -

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Basic information

Entry
Database: PDB / ID: 4ge3
TitleSchizosaccharomyces pombe DJ-1 T114V mutant
ComponentsUncharacterized protein C22E12.03c
KeywordsUNKNOWN FUNCTION / DJ-1/PfpI family
Function / homology
Function and homology information


SUMOylation of transcription cofactors / Aggrephagy / 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: 1.5 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.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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)85,8939
Polymers85,6584
Non-polymers2355
Water15,763875
1
A: Uncharacterized protein C22E12.03c
B: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8913
Polymers42,8292
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-12 kcal/mol
Surface area14970 Å2
MethodPISA
2
C: Uncharacterized protein C22E12.03c
D: Uncharacterized protein C22E12.03c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0026
Polymers42,8292
Non-polymers1734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-12 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.579, 52.075, 82.912
Angle α, β, γ (deg.)89.01, 88.98, 66.55
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21414.594 Da / Num. of mol.: 4 / Mutation: T114V
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.: 3 / 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


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.32 %
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: Jul 12, 2012 / Details: Osmic blue confocal
RadiationMonochromator: osmic blue optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→83 Å / Num. all: 102613 / Num. obs: 102613 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.9 / Num. unique all: 9604 / % possible all: 87.6

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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: 1.5→82.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.448 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement with 4 groups
RfactorNum. reflection% reflectionSelection details
Rfree0.18864 5115 5 %RANDOM
Rwork0.15844 ---
all0.15992 102117 --
obs0.15992 102117 93.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.174 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.24 Å20.34 Å2
2--0.42 Å2-0.16 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.5→82.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 14 875 6825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226478
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9858805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30425.02253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.536151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5941523
X-RAY DIFFRACTIONr_chiral_restr0.1050.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214899
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 386 -
Rwork0.272 6687 -
obs-7073 86.59 %
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)
11.1204-0.4586-0.13621.48431.03622.7697-0.10070.0691-0.16060.1248-0.02770.10830.2732-0.04480.12850.0415-0.02170.03420.0274-0.01650.06462.902412.5158-1.6898
20.9394-0.3215-0.53682.30870.55992.1893-0.0724-0.11830.08610.17960.0876-0.0765-0.16220.0876-0.01520.07680.0073-0.00480.0305-0.00270.02932.527832.588317.3821
31.3133-0.25850.38220.9793-0.26571.59360.0099-0.086-0.04840.039-0.0082-0.02620.08830.075-0.00180.01-0.0031-0.00690.04040.02410.02053.50342.7807-23.5347
41.2625-0.4636-0.23731.15560.09821.67230.03470.08510.0375-0.157-0.01820.0624-0.1099-0.1374-0.01650.02990.0024-0.01330.03660.01880.0215-12.575454.713-42.7032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 191
2X-RAY DIFFRACTION2B1 - 191
3X-RAY DIFFRACTION3C1 - 191
4X-RAY DIFFRACTION4D1 - 191

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