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- PDB-2jli: Atomic resolution structure of the cytoplasmic domain of Yersinia... -

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Basic information

Entry
Database: PDB / ID: 2jli
TitleAtomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a regulatory switch involved in type III secretion
ComponentsYOP PROTEINS TRANSLOCATION PROTEIN
KeywordsPROTEIN TRANSPORT / CELL MEMBRANE / TRANSMEMBRANE / YERSINIA PESTIS / TYPE III SECRETION SYSTEM / PLASMID / MEMBRANE / VIRULENCE / TRANSPORT
Function / homology
Function and homology information


protein secretion / plasma membrane
Similarity search - Function
secretion proteins EscU / name from scop / Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Yop proteins translocation protein U
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.13 Å
AuthorsLountos, G.T. / Austin, B.P. / Nallamsetty, S. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2009
Title: Atomic Resolution Structure of the Cytoplasmic Domain of Yersinia Pestis Yscu, a Regulatory Switch Involved in Type III Secretion.
Authors: Lountos, G.T. / Austin, B.P. / Nallamsetty, S. / Waugh, D.S.
History
DepositionSep 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YOP PROTEINS TRANSLOCATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,3761
Polymers14,3761
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.162, 48.162, 190.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein YOP PROTEINS TRANSLOCATION PROTEIN / YSCU


Mass: 14376.495 Da / Num. of mol.: 1 / Fragment: YSCU CYTOPLASMIC DOMAIN, RESIDUES 220-342
Source method: isolated from a genetically manipulated source
Details: CLEAVED PEPTIDE BOND BETWEEN N263 AND P264 / Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69986
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLEAVED PEPTIDE BOND BETWEEN N263 AND P264

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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: 2.3 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growpH: 9.5 / Details: 100 MM CHESS PH 9.5, 30% V/V PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 49262 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 50.4
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.2 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0057refinement
HKL-3000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.13→41.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.589 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 2506 5.1 %RANDOM
Rwork0.164 ---
obs0.164 46638 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.13→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 0 161 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022862
X-RAY DIFFRACTIONr_bond_other_d0.0030.02584
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.971191
X-RAY DIFFRACTIONr_angle_other_deg1.1331439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7395121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11323.51437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.98915149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.495157
X-RAY DIFFRACTIONr_chiral_restr0.1370.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0481.5533
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0432878
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6463329
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3174.5301
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.13→1.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 185
Rwork0.267 3331

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