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- PDB-5cul: crystal structure of the PscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5cul
Titlecrystal structure of the PscU C-terminal domain
ComponentsTranslocation protein in type III secretion
KeywordsCELL INVASION / secretion system
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
Translocation protein in type III secretion
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBergeron, J.R.C. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Structure of a Type 3 Secretion System (T3SS) Ruler Protein Suggests a Molecular Mechanism for Needle Length Sensing.
Authors: Bergeron, J.R. / Fernandez, L. / Wasney, G.A. / Vuckovic, M. / Reffuveille, F. / Hancock, R.E. / Strynadka, N.C.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translocation protein in type III secretion
B: Translocation protein in type III secretion


Theoretical massNumber of molelcules
Total (without water)28,8692
Polymers28,8692
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-7 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.570, 68.570, 61.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Translocation protein in type III secretion


Mass: 14434.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pscU, PA1690 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I337
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.44 Å3/Da / Density % sol: 14.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1M di-ammonium hydrogen phosphate, 0.1 M sodium acetate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→42.66 Å / Num. obs: 3694 / % possible obs: 99.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.387 / Net I/σ(I): 7.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.799 / Num. unique all: 536 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JLI

2jli


Resolution: 2.9→42.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.79 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 2.042 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22452 161 4.4 %RANDOM
Rwork0.19562 ---
obs0.19701 3533 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.794 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å21.18 Å20 Å2
2--1.18 Å20 Å2
3----3.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 0 6 866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019872
X-RAY DIFFRACTIONr_bond_other_d0.0050.02894
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9711180
X-RAY DIFFRACTIONr_angle_other_deg0.72932030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.3221.39543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69215157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0741515
X-RAY DIFFRACTIONr_chiral_restr0.050.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021968
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 9 -
Rwork0.31 264 -
obs--99.64 %

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