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- PDB-4r2k: Crystal structure of H119A mutant of YdaA (Universal Stress Prote... -

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Basic information

Entry
Database: PDB / ID: 4r2k
TitleCrystal structure of H119A mutant of YdaA (Universal Stress Protein E) from Salmonella typhimurium
ComponentsUniversal stress protein E
KeywordsMETAL BINDING PROTEIN / UNKNOWN FUNCTION / Universal stress protein / HUP domain / Internal Symmetry / Stress tolerance / ATP binding / Zinc binding
Function / homologyRossmann fold - #12370 / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / cytoplasm / Alpha Beta / OXALIC ACID / Universal stress protein E
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBangera, M. / Murthy, M.R.N.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance.
Authors: Bangera, M. / Panigrahi, R. / Sagurthi, S.R. / Savithri, H.S. / Murthy, M.R.
History
DepositionAug 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,97725
Polymers37,2211
Non-polymers1,75624
Water5,855325
1
A: Universal stress protein E
hetero molecules

A: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,95450
Polymers74,4432
Non-polymers3,51148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area13110 Å2
ΔGint-110 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.820, 79.820, 262.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-423-

OXD

21A-616-

HOH

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Components

#1: Protein Universal stress protein E


Mass: 37221.477 Da / Num. of mol.: 1 / Mutation: H119A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / Gene: STM1661, uspE, ydaA uspE STM1661 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8ZP84
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 298 K / Method: under oil, microbatch
Details: 2M Ammonium sulfate, Under oil, Microbatch, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953725 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2012 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 1.97→39.91 Å / Num. obs: 36482 / % possible obs: 100 % / Redundancy: 14.6 % / Rsym value: 0.086
Reflection shellResolution: 1.97→2.07 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.348 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBE2data collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4R2J

4r2j


Resolution: 1.97→39.46 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.692 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22857 1811 5 %RANDOM
Rwork0.1876 ---
obs0.18969 34480 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å2-0 Å2
2--0.87 Å2-0 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 1.97→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 105 325 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192602
X-RAY DIFFRACTIONr_bond_other_d0.0010.022513
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9833527
X-RAY DIFFRACTIONr_angle_other_deg0.89335772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68224.779113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34715419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.041512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
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_it1.341.5491251
X-RAY DIFFRACTIONr_mcbond_other1.341.5451250
X-RAY DIFFRACTIONr_mcangle_it1.9532.3081564
X-RAY DIFFRACTIONr_mcangle_other1.9562.311565
X-RAY DIFFRACTIONr_scbond_it2.481.9211351
X-RAY DIFFRACTIONr_scbond_other2.4031.8711334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.492.6541936
X-RAY DIFFRACTIONr_long_range_B_refined7.12214.7343186
X-RAY DIFFRACTIONr_long_range_B_other7.12214.7433187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.966→2.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 125 -
Rwork0.201 2479 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 23.047 Å / Origin y: -29.847 Å / Origin z: -8.172 Å
111213212223313233
T0.0599 Å2-0.0189 Å2-0.0063 Å2-0.011 Å2-0.0018 Å2--0.0417 Å2
L1.0514 °2-0.9556 °20.4979 °2-2.4246 °2-1.0598 °2--0.9373 °2
S0.1833 Å °-0.0411 Å °-0.0309 Å °0.0354 Å °-0.0563 Å °-0.0259 Å °-0.0103 Å °0.0435 Å °-0.1269 Å °

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