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- PDB-2ab0: Crystal Structure of E. coli protein YajL (ThiJ) -

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Basic information

Entry
Database: PDB / ID: 2ab0
TitleCrystal Structure of E. coli protein YajL (ThiJ)
ComponentsYajL
KeywordsUNKNOWN FUNCTION / DJ-1/ThiJ superfamily / alpha-beta hydrolase fold
Function / homology
Function and homology information


protein repair / protein deglycase / protein deglycase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / ribosome biogenesis / cellular response to oxidative stress / response to heat / protein refolding / DNA repair ...protein repair / protein deglycase / protein deglycase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / ribosome biogenesis / cellular response to oxidative stress / response to heat / protein refolding / DNA repair / protein homodimerization activity / cytosol / cytoplasm
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
Protein/nucleic acid deglycase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsWilson, M.A. / Ringe, D. / Petsko, G.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Atomic Resolution Crystal Structure of the YajL (ThiJ) Protein from Escherichia coli: A Close Prokaryotic Homologue of the Parkinsonism-associated Protein DJ-1.
Authors: Wilson, M.A. / Ringe, D. / Petsko, G.A.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YajL
B: YajL


Theoretical massNumber of molelcules
Total (without water)43,9952
Polymers43,9952
Non-polymers00
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-15 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.722, 78.475, 99.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a dimer generated from chain A and chain B after application of the following operation to chain B: -x+1, y+1/2, -z-1/2

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Components

#1: Protein YajL


Mass: 21997.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thiJ / Plasmid: pET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q46948
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 1.98 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Tris-HCl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.86 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2004
RadiationMonochromator: BENT Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.1→100 Å / Num. all: 136923 / Num. obs: 132051 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 9.23 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 33.27
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.24 / Num. unique all: 13484 / % possible all: 92.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5F

1p5f


Resolution: 1.1→100 Å / Num. parameters: 31888 / Num. restraintsaints: 41370 / Isotropic thermal model: Babinet / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1706 6607 5 %RANDOM
Rwork0.1363 ---
all0.1366 132051 --
obs0.1366 132051 96.6 %-
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 2908.98 / Occupancy sum non hydrogen: 3342
Refinement stepCycle: LAST / Resolution: 1.1→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 0 440 3538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.109

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