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- PDB-5cb0: Crystal structure and functional implications of the tandem-type ... -

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Basic information

Entry
Database: PDB / ID: 5cb0
TitleCrystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli
ComponentsUniversal stress protein E
KeywordsUNKNOWN FUNCTION / UspE / UspA superfamily / Enterohemorrhagic Escherichia coli
Function / homology
Function and homology information


single-species biofilm formation / small molecule binding / response to stress / bacterial-type flagellum-dependent cell motility / cellular response to hydrogen peroxide / cellular response to UV / cytoplasm
Similarity search - Function
Rossmann fold - #12370 / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxotetradecanoic acid / Universal stress protein E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.207 Å
AuthorsXu, Y. / Quan, C.S. / Jin, X. / Jin, L. / Kim, J.S. / Guo, J. / Fan, S. / Ha, N.C.
Funding support China, 2items
OrganizationGrant numberCountry
The National Natural Science Foundation of China31200556 China
the China Postdoctoral Science Foundation2013M540229 China
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli.
Authors: Xu, Y. / Guo, J. / Jin, X. / Kim, J.S. / Ji, Y. / Fan, S. / Ha, N.C. / Quan, C.S.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Universal stress protein E
B: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9804
Polymers71,4962
Non-polymers4852
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-20 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.134, 121.134, 241.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Universal stress protein E


Mass: 35747.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uspE, ydaA, b1333, JW1327 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAC0
#2: Chemical ChemComp-Z6X / 3-oxotetradecanoic acid


Mass: 242.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26O3

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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: 3.1 Å3/Da / Density % sol: 60.37 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 288 K / Method: evaporation / pH: 6.5
Details: 10% 1.4-dioxane, 1.6 M ammonium sulfate, 0.1 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→19.9 Å / Num. all: 16684 / Num. obs: 16684 / % possible obs: 90.2 % / Redundancy: 3.6 % / Net I/σ(I): 3.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OLQ

3olq


Resolution: 3.207→19.9 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.53 / Phase error: 29.47 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.3006 1313 10.03 %
Rwork0.2431 --
obs0.2489 13096 46.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.207→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 34 0 4665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074776
X-RAY DIFFRACTIONf_angle_d1.3936489
X-RAY DIFFRACTIONf_dihedral_angle_d16.7011791
X-RAY DIFFRACTIONf_chiral_restr0.059721
X-RAY DIFFRACTIONf_plane_restr0.009841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2074-3.33580.3409820.2618730X-RAY DIFFRACTION26
3.3358-3.48760.34421060.2774965X-RAY DIFFRACTION34
3.4876-3.67140.34981360.27391221X-RAY DIFFRACTION43
3.6714-3.90130.35031520.27911365X-RAY DIFFRACTION48
3.9013-4.20230.30591530.24471382X-RAY DIFFRACTION50
4.2023-4.62480.33581650.22411479X-RAY DIFFRACTION52
4.6248-5.29310.27771650.2291490X-RAY DIFFRACTION53
5.2931-6.66530.26581690.261514X-RAY DIFFRACTION54
6.6653-44.96220.27151850.2221637X-RAY DIFFRACTION58

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