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- PDB-7eva: Structure of molecular chaperone SycE of Yersinia enterocolitica -

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Basic information

Entry
Database: PDB / ID: 7eva
TitleStructure of molecular chaperone SycE of Yersinia enterocolitica
ComponentsYopE regulator
KeywordsCHAPERONE / Molecular-chaperone / Yersinia Outer Protein / Type Three secrection chaperone
Function / homologyType III secretion chaperone SycE / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / protein secretion by the type III secretion system / YopE regulator
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.083 Å
AuthorsKumar, R. / Datta, S.
CitationJournal: To Be Published
Title: Structure of molecular chaperone SycE of Yersinia enterocolitica
Authors: Kumar, R. / Datta, S.
History
DepositionMay 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
C: YopE regulator


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water1,35175
1
C: YopE regulator

C: YopE regulator


Theoretical massNumber of molelcules
Total (without water)33,8282
Polymers33,8282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2810 Å2
ΔGint-19 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 58.000, 77.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YopE regulator


Mass: 16914.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: sycE, yerA, ERS008652_03695, NCTC10938_04290 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q79NJ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.91 Å3/Da / Density % sol: 35.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM MES pH 6.0, 50-80mM Na-Citrate, 5-10% PEG 3350, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Mar 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.08→25.94 Å / Num. obs: 8342 / % possible obs: 99.7 % / Redundancy: 15.11 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 1.51
Reflection shellResolution: 2.08→2.14 Å / Rmerge(I) obs: 0.278 / Num. unique obs: 8342

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Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
PROTEUM PLUS1.15.2_3472data scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHENIX1.15.2-3472-000refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n5b

1n5b


Resolution: 2.083→25.938 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 382 4.6 %
Rwork0.1995 7922 -
obs0.201 8304 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.81 Å2 / Biso mean: 31.2664 Å2 / Biso min: 12.16 Å2
Refinement stepCycle: final / Resolution: 2.083→25.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 0 75 1011
Biso mean---33.82 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.083-2.38380.26221120.1895255499
2.3838-3.00260.24261490.20342596100
3.0026-3.00260.22091210.20092772100

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