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- PDB-5sy4: Atomic resolution structure of reduced E. coli YajL -

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Basic information

Entry
Database: PDB / ID: 5sy4
TitleAtomic resolution structure of reduced E. coli YajL
ComponentsChaperone YajL
KeywordsCHAPERONE / DJ-1/PfpI superfamily nucleophile elbow
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 / cytoplasm / cytosol
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 / protein deglycase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsWilson, M.A. / Lin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM092999 United States
CitationJournal: Biochemistry / Year: 2017
Title: Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.
Authors: Lin, J. / Pozharski, E. / Wilson, M.A.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,2094
Polymers42,1612
Non-polymers492
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-24 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.875, 78.313, 99.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 196 / Label seq-ID: 5 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W8T6D9, UniProt: Q46948*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: polyethylene glycol 4000, Tris HCl, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.73 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2015
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73 Å / Relative weight: 1
ReflectionResolution: 0.98→38 Å / Num. obs: 191363 / % possible obs: 97.6 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.9
Reflection shellResolution: 0.98→1 Å / Redundancy: 9.5 % / Rmerge(I) obs: 2.393 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.479 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AB0

2ab0


Resolution: 0.98→61.52 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.663 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1266 3842 2 %RANDOM
Rwork0.11403 ---
obs0.11427 187313 97.34 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.354 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 0.98→61.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 2 426 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193635
X-RAY DIFFRACTIONr_bond_other_d0.0030.023553
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.985001
X-RAY DIFFRACTIONr_angle_other_deg1.18338232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29824.593135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83415616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3521519
X-RAY DIFFRACTIONr_chiral_restr0.1640.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214287
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02760
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0590.9531911
X-RAY DIFFRACTIONr_mcbond_other1.0490.9531910
X-RAY DIFFRACTIONr_mcangle_it1.4481.4352447
X-RAY DIFFRACTIONr_mcangle_other1.4491.4362448
X-RAY DIFFRACTIONr_scbond_it1.7971.2391724
X-RAY DIFFRACTIONr_scbond_other1.7451.2361721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1191.7662554
X-RAY DIFFRACTIONr_long_range_B_refined3.17113.1144106
X-RAY DIFFRACTIONr_long_range_B_other2.48712.4454005
X-RAY DIFFRACTIONr_rigid_bond_restr3.44937188
X-RAY DIFFRACTIONr_sphericity_free38.4775274
X-RAY DIFFRACTIONr_sphericity_bonded8.70657249
Refine LS restraints NCS

Ens-ID: 1 / Number: 14130 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 287 -
Rwork0.294 13412 -
obs--95.21 %

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