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- PDB-4fqb: crystal structure of toxic effector Tse1 in complex with immune p... -

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Basic information

Entry
Database: PDB / ID: 4fqb
Titlecrystal structure of toxic effector Tse1 in complex with immune protein Tsi1
Components
  • immune protein Tsi1Immunity (medical)
  • toxic effector Tse1
KeywordsTOXIN/IMMUNE SYSTEM / beta sheet / toxic effector with immune protein / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane
Similarity search - Function
Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lipocalin / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Beta Barrel ...Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lipocalin / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immune protein Tsi1 / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsWang, T. / Li, L. / Zhang, W.
CitationJournal: To be Published
Title: structural basis of Tse1 in complex with Tsi1
Authors: Li, L. / Zhang, W. / Wang, T.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: toxic effector Tse1
B: immune protein Tsi1
C: toxic effector Tse1
D: immune protein Tsi1
E: toxic effector Tse1
F: immune protein Tsi1
G: toxic effector Tse1
H: immune protein Tsi1


Theoretical massNumber of molelcules
Total (without water)142,3518
Polymers142,3518
Non-polymers00
Water1,29772
1
A: toxic effector Tse1
B: immune protein Tsi1


Theoretical massNumber of molelcules
Total (without water)35,5882
Polymers35,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-4 kcal/mol
Surface area13410 Å2
MethodPISA
2
C: toxic effector Tse1
D: immune protein Tsi1


Theoretical massNumber of molelcules
Total (without water)35,5882
Polymers35,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-4 kcal/mol
Surface area13370 Å2
MethodPISA
3
E: toxic effector Tse1
F: immune protein Tsi1


Theoretical massNumber of molelcules
Total (without water)35,5882
Polymers35,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-2 kcal/mol
Surface area13380 Å2
MethodPISA
4
G: toxic effector Tse1
H: immune protein Tsi1


Theoretical massNumber of molelcules
Total (without water)35,5882
Polymers35,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-2 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.710, 97.710, 293.301
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.823381, -0.104279, 0.557825), (-0.110474, -0.934712, -0.3378), (0.556631, -0.339764, 0.758104)10.11087, 17.12139, 0.86033
3given(0.767203, -0.306086, -0.563658), (-0.238761, -0.951919, 0.191945), (-0.595309, -0.012682, -0.803397)-31.10011, -56.83527, -64.38976
4given(-0.937735, 0.34685, 0.018658), (0.336986, 0.895413, 0.290991), (0.084223, 0.27916, -0.956544)-43.09138, 12.96126, -39.46775
Details1:1 in complex with Tsi1

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Components

#1: Protein
toxic effector Tse1


Mass: 17529.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1844 / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1
#2: Protein
immune protein Tsi1 / Immunity (medical)


Mass: 18057.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1845 / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9I2Q0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 100mM Sodium Citrate, 20% V/V 2-propanol, 20% W/V PEG4000,1mM DTT, 3% V/V Ethylene Glycol, pH 5.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.009 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 1, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. all: 43259 / Num. obs: 43188 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / Num. unique all: 6623 / % possible all: 100

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Processing

Software
NameVersionClassification
SSRF-scriptdata collection
PHENIXmodel building
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FQA

4fqa


Resolution: 2.69→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 26.308 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.774 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24546 2201 5.1 %RANDOM
Rwork0.20118 ---
obs0.20337 40994 93.59 %-
all-43188 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.574 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.78 Å20 Å2
2--1.56 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8932 0 0 72 9004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.811.94212415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52551174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73324.326430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.174151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.621564
X-RAY DIFFRACTIONr_chiral_restr0.1090.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217128
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 134 -
Rwork0.373 2899 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8868-0.9865-1.84767.46542.66046.597-0.0870.60190.0979-0.64820.2541-1.5374-0.13680.447-0.16710.4024-0.35580.08380.42090.02920.3992.237-17.067-33.548
24.55280.8755-1.46926.265-0.66326.40610.0121-0.20980.28730.36450.0326-0.0334-0.1959-0.2898-0.04470.3931-0.2794-0.10040.26620.05890.0442-12.674-7.244-12.978
35.8639-1.21210.6517.2683-1.05883.80230.01630.30980.20310.23810.12041.67120.0269-0.878-0.13680.397-0.25470.17110.43860.05060.7551-8.83844.309-19.086
46.23011.50171.10793.8213-0.16864.72090.12560.1577-0.33540.08660.0103-0.01330.07940.2416-0.13590.4071-0.23320.09170.163-0.05030.102313.86930.204-14.746
514.59223.84732.08638.53322.13845.5325-0.1070.0699-0.46540.2936-0.0855-1.33760.24390.74590.19250.412-0.2728-0.01220.42130.00920.5262-2.367-48.618-35.807
610.1623-1.4248-0.0994.862-0.40325.4121-0.0060.3113-0.0255-0.0222-0.17970.00560.0851-0.16320.18570.3674-0.25190.08720.24-0.11280.0724-28.342-53.135-41.816
77.12172.4275-4.03267.4567-0.8697.01230.06-0.33940.62260.86810.01841.4206-0.3111-0.6462-0.07840.6507-0.05180.28120.47430.07550.6637-51.983-9.374-13.472
86.26160.666-0.94054.3057-0.436.83020.01210.12070.67810.452-0.00540.256-0.62710.0144-0.00680.2913-0.1104-0.05790.24680.14050.1643-33.184-0.391-30.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2B21 - 169
3X-RAY DIFFRACTION3C4 - 149
4X-RAY DIFFRACTION4D23 - 169
5X-RAY DIFFRACTION5E4 - 149
6X-RAY DIFFRACTION6F23 - 169
7X-RAY DIFFRACTION7G4 - 149
8X-RAY DIFFRACTION8H23 - 169

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