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- PDB-1yj7: Crystal structure of enteropathogenic E.coli (EPEC) type III secr... -

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Basic information

Entry
Database: PDB / ID: 1yj7
TitleCrystal structure of enteropathogenic E.coli (EPEC) type III secretion system protein EscJ
ComponentsescJ
KeywordsPROTEIN TRANSPORT / mixed alpha/beta / extended linker
Function / homology
Function and homology information


protein secretion / cell outer membrane
Similarity search - Function
Hypothetical protein rpa1041 / Type III secretion system lipoprotein HrcJ/YscJ / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / ANL, C-terminal domain / GMP Synthetase; Chain A, domain 3 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Lipoprotein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsYip, C.K. / Kimbrough, T.G. / Felise, H.B. / Vuckovic, M. / Thomas, N.A. / Pfuetzner, R.A. / Frey, E.A. / Finlay, B.B. / Miller, S.I. / Strynadka, N.C.J.
CitationJournal: Nature / Year: 2005
Title: Structural characterization of the molecular platform for type III secretion system assembly.
Authors: Yip, C.K. / Kimbrough, T.G. / Felise, H.B. / Vuckovic, M. / Thomas, N.A. / Pfuetzner, R.A. / Frey, E.A. / Finlay, B.B. / Miller, S.I. / Strynadka, N.C.
History
DepositionJan 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: escJ
B: escJ
C: escJ
D: escJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63610
Polymers74,0724
Non-polymers5646
Water9,548530
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.817, 164.817, 67.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is the tetramer in the asymmetric unit.

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Components

#1: Protein
escJ


Mass: 18518.021 Da / Num. of mol.: 4
Fragment: signal peptide-removed and non-lipidated, residues 21-190
Mutation: E62A, K63A, E64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EscJ / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8VQD3
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.2
Details: di-ammonium hydrogen phosphate, pH 8.2, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2004 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→41.17 Å / Num. obs: 96428 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALAdata scaling
SOLVEphasing
CNS& Refmac5.1refinement
CCP4(SCALA)data scaling
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→41.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.206 4826 random
Rwork0.184 --
all0.185 --
obs0.185 91589 -
Displacement parametersBiso mean: 19.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 0 32 530 5271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.232
X-RAY DIFFRACTIONr_bond_other_d0.002
X-RAY DIFFRACTIONr_angle_other_deg0.752
X-RAY DIFFRACTIONr_gen_planes_refined0.004
LS refinement shellResolution: 1.8→1.847 Å
RfactorNum. reflection
Rfree0.249 371
Rwork0.214 -
obs-6726

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