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- PDB-2uwj: Structure of the heterotrimeric complex which regulates type III ... -

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Basic information

Entry
Database: PDB / ID: 2uwj
TitleStructure of the heterotrimeric complex which regulates type III secretion needle formation
Components
  • TYPE III EXPORT PROTEIN PSCE
  • TYPE III EXPORT PROTEIN PSCF
  • TYPE III EXPORT PROTEIN PSCG
KeywordsCHAPERONE / VIRULENCE / CHAPERONES / COILED COIL / NEEDLE FORMATION / TYPE III SECRETION / BACTERIAL PATHOGENICITY
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / : / extracellular region / cytoplasm
Similarity search - Function
Type III secretion system YscG / Bacterial type II secretion system chaperone protein (type_III_yscG) / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Immunoglobulin FC, subunit C / Tetratricopeptide repeat domain ...Type III secretion system YscG / Bacterial type II secretion system chaperone protein (type_III_yscG) / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Immunoglobulin FC, subunit C / Tetratricopeptide repeat domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Type III needle protein PscF / Type III export protein PscG / Type III export protein PscE
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsQuinaud, M. / Ple, S. / Job, V. / Contreras-Martel, C. / Simorre, J.P. / Attree, I. / Dessen, A.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2007
Title: Structure of the heterotrimeric complex that regulates type III secretion needle formation.
Authors: Quinaud, M. / Ple, S. / Job, V. / Contreras-Martel, C. / Simorre, J.P. / Attree, I. / Dessen, A.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: The Psce-Pscf-Pscg Complex Controls Type III Secretion Needle Biogenesis in Pseudomonas Aeruginosa
Authors: Quinaud, M. / Chabert, J. / Faudry, E. / Neumann, E. / Lemaire, D. / Pastor, A. / Elsen, S. / Dessen, A. / Attree, I.
History
DepositionMar 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TYPE III EXPORT PROTEIN PSCE
F: TYPE III EXPORT PROTEIN PSCF
G: TYPE III EXPORT PROTEIN PSCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0636
Polymers23,8873
Non-polymers1763
Water3,099172
1
E: TYPE III EXPORT PROTEIN PSCE
F: TYPE III EXPORT PROTEIN PSCF
G: TYPE III EXPORT PROTEIN PSCG
hetero molecules

E: TYPE III EXPORT PROTEIN PSCE
F: TYPE III EXPORT PROTEIN PSCF
G: TYPE III EXPORT PROTEIN PSCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,12712
Polymers47,7756
Non-polymers3526
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)85.305, 85.305, 157.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein TYPE III EXPORT PROTEIN PSCE / PSCE / PSEUDOMONAS SECRETION PROTEIN E


Mass: 7631.673 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: CHA / Plasmid: PET-15B (NOVAGEN) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I317
#2: Protein/peptide TYPE III EXPORT PROTEIN PSCF / PSCF / PSEUDOMONAS SECRETION PROTEIN F


Mass: 3791.535 Da / Num. of mol.: 1 / Fragment: RESIDUES 54-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: CHA / Plasmid: PET-15B (NOVAGEN) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95434
#3: Protein TYPE III EXPORT PROTEIN PSCG / PSCG / PSEUDOMONAS SECRETION PROTEIN G


Mass: 12464.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: CHA / Plasmid: PET-15B (NOVAGEN) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95435
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GSH TAG REMAINING RESIDUES THE DNA SEQUENCE CORRESPONDING TO THE FIRST 54 RESIDUES OF ...N-TERMINAL GSH TAG REMAINING RESIDUES THE DNA SEQUENCE CORRESPONDING TO THE FIRST 54 RESIDUES OF PSCF WAS REMOVED FROM THE PSCEFG SEQUENCE.

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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: 3.47 Å3/Da / Density % sol: 64.57 % / Description: HEAVY ATOM SEARCH USING SHELXD
Crystal growpH: 7.4 / Details: 0.1M TRIS HCL PH 7.4, 0.8M LISO4, 10MM NICL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 27335 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 70.1 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2034355.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: PSCG FOLDS AS A TPR LIKE DOMAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1146 4.9 %RANDOM
Rwork0.208 ---
obs0.208 23525 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.0325 Å2 / ksol: 0.383092 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.97 Å24.41 Å20 Å2
2--4.97 Å20 Å2
3----9.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 3 172 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.281.5
X-RAY DIFFRACTIONc_mcangle_it4.132
X-RAY DIFFRACTIONc_scbond_it5.342
X-RAY DIFFRACTIONc_scangle_it7.292.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 208 5.4 %
Rwork0.238 3625 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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