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- PDB-1k3e: Type III secretion chaperone CesT -

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Basic information

Entry
Database: PDB / ID: 1k3e
TitleType III secretion chaperone CesT
ComponentsCesT
KeywordsCHAPERONE / Secretion / Type III / intimin receptor
Function / homology
Function and homology information


protein secretion by the type III secretion system / : / cytoplasm
Similarity search - Function
Helix Hairpins - #390 / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tir chaperone / Tir chaperone
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLuo, Y. / Bertero, M. / Frey, E.A. / Pfuetzner, R.A. / Wenk, M.R. / Creagh, L. / Marcus, S.L. / Lim, D. / Finlay, B.B. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structural and biochemical characterization of the type III secretion chaperones CesT and SigE.
Authors: Luo, Y. / Bertero, M.G. / Frey, E.A. / Pfuetzner, R.A. / Wenk, M.R. / Creagh, L. / Marcus, S.L. / Lim, D. / Sicheri, F. / Kay, C. / Haynes, C. / Finlay, B.B. / Strynadka, N.C.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Source and taxonomy
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CesT
B: CesT


Theoretical massNumber of molelcules
Total (without water)35,3902
Polymers35,3902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-21 kcal/mol
Surface area17480 Å2
MethodPISA
2
A: CesT

B: CesT


Theoretical massNumber of molelcules
Total (without water)35,3902
Polymers35,3902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area4560 Å2
ΔGint-23 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.586, 77.856, 94.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CesT


Mass: 17694.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This sequence occurs naturally in Escherichia coli O157:H7.
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: cesT / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47015, UniProt: P58233*PLUS

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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: 2.96 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 10% PEG 600, 1.5 M ammonium sulfate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, temperature 291.0K
Crystal grow
*PLUS
pH: 8.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl11pH8.2
320 mg/mlprotein11
41.3-1.8 Mammonium sulfate12pH5.4-6.2
211NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 10823 / Num. obs: 10290 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 25.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 6.2 / Num. unique all: 773 / Rsym value: 0.151 / % possible all: 72.2
Reflection
*PLUS
Num. measured all: 43030
Reflection shell
*PLUS
% possible obs: 72.2 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.8→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1022 9.2 %RANDOM
Rwork0.225 ---
all-10823 --
obs-9957 92 %-
Displacement parametersBiso mean: 65.25 Å2
Baniso -1Baniso -2Baniso -3
1--36.158 Å20 Å20 Å2
2--20.385 Å20 Å2
3---15.774 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 0 0 2254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.484
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 9.2 % / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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