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- PDB-4r2j: Crystal structure of YdaA (Universal Stress Protein E) from Salmo... -

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Basic information

Entry
Database: PDB / ID: 4r2j
TitleCrystal structure 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
Function / homology
Function and homology information


Rossmann fold - #12370 / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / PHOSPHATE ION / Universal stress protein E
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 24, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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)37,8716
Polymers37,2891
Non-polymers5835
Water61334
1
A: Universal stress protein E
hetero molecules

A: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,74312
Polymers74,5772
Non-polymers1,16610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3310 Å2
ΔGint-76 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.770, 85.770, 74.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Universal stress protein E


Mass: 37288.547 Da / Num. of mol.: 1
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
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 37 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: under oil, microbatch / pH: 5.8
Details: 0.2M Magnesium Nitrate hexahydrate, 20% PEG 3350, 10mM Adenosine 5'-(beta,gamma-imido)triphosphate, 0.2% n-dodecyl beta-D-maltoside, pH 5.8, Under oil, Microbatch, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2011 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.36→42.88 Å / Num. obs: 13536 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.119
Reflection shellResolution: 2.36→2.48 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1929 / Rsym value: 0.642 / % possible all: 98.9

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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 3OLQ

3olq


Resolution: 2.36→37.14 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.386 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26186 667 4.9 %RANDOM
Rwork0.21193 ---
obs0.21435 12849 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20.57 Å2-0 Å2
2--1.15 Å2-0 Å2
3----3.72 Å2
Refinement stepCycle: LAST / Resolution: 2.36→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 34 34 2183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192192
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9663001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78424.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71215311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.201159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211628
X-RAY DIFFRACTIONr_mcbond_it2.6783.9621135
X-RAY DIFFRACTIONr_mcangle_it3.9515.9231410
X-RAY DIFFRACTIONr_scbond_it3.8764.2381057
X-RAY DIFFRACTIONr_long_range_B_refined7.26334.2513270
LS refinement shellResolution: 2.356→2.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 46 -
Rwork0.286 913 -
obs--97.66 %
Refinement TLS params.Method: refined / Origin x: 25.405 Å / Origin y: 16.474 Å / Origin z: 6.161 Å
111213212223313233
T0.0991 Å20.0238 Å2-0.0514 Å2-0.0267 Å20.0092 Å2--0.0689 Å2
L1.4166 °2-0.4553 °2-0.6366 °2-2.1973 °20.486 °2--6.5914 °2
S0.0708 Å °-0.0436 Å °-0.0478 Å °-0.0941 Å °-0.0055 Å °0.0883 Å °0.3938 Å °0.0236 Å °-0.0653 Å °

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