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- PDB-9yfs: Protiated E. coli YajL, 100K -

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Basic information

Entry
Database: PDB / ID: 9yfs
TitleProtiated E. coli YajL, 100K
ComponentsChaperone YajL
KeywordsHYDROLASE / Hydolase
Function / homologyProtein/nucleic acid deglycase DJ-1 / protein deglycase / protein deglycase activity / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / cytoplasm / DJ-1 family protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 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
DepositionSep 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chaperone YajL
A: Chaperone YajL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2806
Polymers42,1612
Non-polymers1204
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-40 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.767, 78.474, 99.616
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 Chaperone YajL / DJ-1 family protein / Oxidative-stress-resistance chaperone


Mass: 21080.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: thiJ, ACU57_11870, AM266_04520, ERS085365_02411, ERS085416_01937, ERS139211_01908, ERS150873_01827, PU15_11320, PU38_04800, SK85_00449
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8T6D9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 19-22% PEG 4000, 225 mM MgCl2, and 100 mM Tris HCl, pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.729 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 0.94→39.24 Å / Num. obs: 222540 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 9.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 0.94→0.96 Å / Num. unique obs: 10804 / CC1/2: 0.303

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.94→39.24 Å / SU ML: 0.0972 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.137 6568 2.97 %
Rwork0.1207 214346 -
obs0.1212 220914 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.21 Å2
Refinement stepCycle: LAST / Resolution: 0.94→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 4 614 3520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783474
X-RAY DIFFRACTIONf_angle_d1.08124796
X-RAY DIFFRACTIONf_chiral_restr0.0922572
X-RAY DIFFRACTIONf_plane_restr0.0101636
X-RAY DIFFRACTIONf_dihedral_angle_d11.52451308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.950.38111870.3586093X-RAY DIFFRACTION85.15
0.95-0.960.33552060.34296809X-RAY DIFFRACTION96.08
0.96-0.970.34262400.31587034X-RAY DIFFRACTION98.38
0.97-0.990.33251960.29777064X-RAY DIFFRACTION99.23
0.99-10.30242050.27997144X-RAY DIFFRACTION99.42
1-1.010.29331940.26957092X-RAY DIFFRACTION99.64
1.01-1.030.27992030.24677148X-RAY DIFFRACTION99.82
1.03-1.040.23372250.21577167X-RAY DIFFRACTION99.93
1.04-1.060.21272290.19487086X-RAY DIFFRACTION99.9
1.06-1.080.17012380.17717143X-RAY DIFFRACTION99.92
1.08-1.090.20592220.16197186X-RAY DIFFRACTION99.93
1.09-1.110.16092280.14477104X-RAY DIFFRACTION99.95
1.11-1.140.14852480.13657106X-RAY DIFFRACTION99.95
1.14-1.160.13782020.12397159X-RAY DIFFRACTION99.85
1.16-1.180.14762270.12397189X-RAY DIFFRACTION99.88
1.18-1.210.13172240.10987152X-RAY DIFFRACTION99.89
1.21-1.240.12291820.10867200X-RAY DIFFRACTION99.96
1.24-1.280.1272130.10367168X-RAY DIFFRACTION99.93
1.28-1.310.12031980.10467205X-RAY DIFFRACTION99.95
1.31-1.360.11782180.0967182X-RAY DIFFRACTION99.95
1.36-1.40.10782360.09137205X-RAY DIFFRACTION99.97
1.4-1.460.10932110.08867200X-RAY DIFFRACTION99.84
1.46-1.530.10951990.08187246X-RAY DIFFRACTION99.96
1.53-1.610.10412390.08247191X-RAY DIFFRACTION99.96
1.61-1.710.10552280.0827218X-RAY DIFFRACTION100
1.71-1.840.11032500.08637256X-RAY DIFFRACTION100
1.84-2.020.10492130.08937277X-RAY DIFFRACTION99.95
2.02-2.320.11032220.09047323X-RAY DIFFRACTION99.91
2.32-2.920.12142220.10927381X-RAY DIFFRACTION100
2.92-39.240.13442630.12767618X-RAY DIFFRACTION99.89

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