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- PDB-9ykf: Crystal Structure of E. coli D23N YajL -

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Basic information

Entry
Database: PDB / ID: 9ykf
TitleCrystal Structure of E. coli D23N YajL
ComponentsProtein/nucleic acid deglycase 3
KeywordsHYDROLASE / DJ-1 superfamily / Cysteine dependent enzyme
Function / homology
Function and homology information


protein deglycase / protein deglycase activity / protein repair / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / ribosome biogenesis / response to heat / protein refolding / cellular response to oxidative stress / DNA repair ...protein deglycase / protein deglycase activity / protein repair / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / ribosome biogenesis / response to heat / protein refolding / cellular response to oxidative stress / 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-like
Similarity search - Domain/homology
Protein/nucleic acid deglycase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsLin, J. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153337 United States
Citation
Journal: To Be Published
Title: Environmental contributions to proton sharing in protein low barrier hydrogen bonds
Authors: Lin, J. / Gerlits, O. / Kneller, D.W. / Weiss, K.L. / Coates, L. / Hix, M.A. / Effah, S.Y. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein/nucleic acid deglycase 3
B: Protein/nucleic acid deglycase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,78116
Polymers42,1592
Non-polymers62314
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-65 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.723, 78.335, 99.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein/nucleic acid deglycase 3 / Chaperone protein YajL / Maillard deglycase


Mass: 21079.334 Da / Num. of mol.: 2 / Mutation: D23N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yajL, thiJ, b0424, JW5057 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q46948, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 22-25% PEG 4000, 200 mM MgCl2, and 100 mM Tris, pH=8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 0.98→40.04 Å / Num. obs: 194272 / % possible obs: 99 % / Redundancy: 7.7 % / Biso Wilson estimate: 7.84 Å2 / CC1/2: 1 / Rrim(I) all: 0.048 / Net I/σ(I): 20.5
Reflection shellResolution: 0.98→1 Å / Num. unique obs: 8354 / CC1/2: 0.754 / Rrim(I) all: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→39.17 Å / SU ML: 0.0658 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 8.5239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1144 5856 3.02 %
Rwork0.0969 188297 -
obs0.0974 194153 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.07 Å2
Refinement stepCycle: LAST / Resolution: 0.98→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 32 576 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833743
X-RAY DIFFRACTIONf_angle_d1.13715165
X-RAY DIFFRACTIONf_chiral_restr0.0898604
X-RAY DIFFRACTIONf_plane_restr0.0114689
X-RAY DIFFRACTIONf_dihedral_angle_d11.74391418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.22521690.21745323X-RAY DIFFRACTION84.86
0.99-10.19132190.18155654X-RAY DIFFRACTION91.05
1-1.010.17042010.15946193X-RAY DIFFRACTION98.14
1.01-1.030.16881840.1446269X-RAY DIFFRACTION99.97
1.03-1.040.15491890.13856331X-RAY DIFFRACTION99.94
1.04-1.060.17331970.13996250X-RAY DIFFRACTION99.88
1.06-1.070.14032000.12226296X-RAY DIFFRACTION99.92
1.07-1.090.12491990.10986263X-RAY DIFFRACTION99.69
1.09-1.10.1171570.09716290X-RAY DIFFRACTION99.75
1.1-1.120.11511920.08546322X-RAY DIFFRACTION99.28
1.12-1.140.09362020.07796220X-RAY DIFFRACTION99.91
1.14-1.160.09631820.07536330X-RAY DIFFRACTION99.92
1.16-1.180.09312310.07516291X-RAY DIFFRACTION99.88
1.18-1.210.0971910.07466291X-RAY DIFFRACTION99.85
1.21-1.230.08752010.07496241X-RAY DIFFRACTION99.61
1.23-1.260.09142010.07526336X-RAY DIFFRACTION99.42
1.26-1.290.08571890.0796248X-RAY DIFFRACTION99.44
1.29-1.330.10031860.07636333X-RAY DIFFRACTION99.89
1.33-1.370.09022000.07456301X-RAY DIFFRACTION99.85
1.37-1.410.09291870.0716357X-RAY DIFFRACTION99.82
1.41-1.460.08991890.07176302X-RAY DIFFRACTION99.75
1.46-1.520.0881840.07356343X-RAY DIFFRACTION99.44
1.52-1.590.10032000.07416274X-RAY DIFFRACTION99.13
1.59-1.680.08632150.07596386X-RAY DIFFRACTION99.94
1.68-1.780.10211860.0816362X-RAY DIFFRACTION99.95
1.78-1.920.10161870.08566423X-RAY DIFFRACTION99.95
1.92-2.110.08611930.08736396X-RAY DIFFRACTION99.62
2.11-2.420.09341980.0936427X-RAY DIFFRACTION99.62
2.42-3.040.12852130.11226494X-RAY DIFFRACTION99.94
3.04-39.170.15642140.12546751X-RAY DIFFRACTION99.83

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