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- PDB-4fgi: Structure of the effector - immunity system Tse1 / Tsi1 from Pseu... -

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Basic information

Entry
Database: PDB / ID: 4fgi
TitleStructure of the effector - immunity system Tse1 / Tsi1 from Pseudomonas aeruginosa
Components
  • Tse1
  • Tsi1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / N1pC/P60 superfamily for Tse1 / type IV dipeptidyl peptidase for Tsi1 / effector immunity protein complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR 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) / Papain-like cysteine peptidase superfamily / Lipocalin / Alpha-Beta Complex / Beta Barrel ...Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Lipocalin / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsBenz, J. / Sendlmeier, C. / Barends, T.R.M. / Meinhart, A.
CitationJournal: Plos One / Year: 2012
Title: Structural Insights into the Effector - Immunity System Tse1/Tsi1 from Pseudomonas aeruginosa.
Authors: Benz, J. / Sendlmeier, C. / Barends, T.R. / Meinhart, A.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tse1
B: Tsi1
C: Tse1
D: Tsi1
E: Tse1
F: Tsi1
G: Tse1
H: Tsi1


Theoretical massNumber of molelcules
Total (without water)139,1438
Polymers139,1438
Non-polymers00
Water00
1
A: Tse1
B: Tsi1


Theoretical massNumber of molelcules
Total (without water)34,7862
Polymers34,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-3 kcal/mol
Surface area13550 Å2
MethodPISA
2
C: Tse1
D: Tsi1


Theoretical massNumber of molelcules
Total (without water)34,7862
Polymers34,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4 kcal/mol
Surface area13590 Å2
MethodPISA
3
E: Tse1
F: Tsi1


Theoretical massNumber of molelcules
Total (without water)34,7862
Polymers34,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-3 kcal/mol
Surface area13440 Å2
MethodPISA
4
G: Tse1
H: Tsi1


Theoretical massNumber of molelcules
Total (without water)34,7862
Polymers34,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-5 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.560, 97.560, 423.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1 / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA4 - 1484 - 148
21LEULEUCC4 - 1484 - 148
31LEULEUEE4 - 1484 - 148
41LEULEUGG4 - 1484 - 148
12ALAALABB23 - 1672 - 146
22ALAALADD23 - 1672 - 146
32ALAALAFF23 - 1672 - 146
42ALAALAHH23 - 1672 - 146

NCS ensembles :
ID
1
2

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Components

#1: Protein
Tse1


Mass: 17930.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1844 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9I2Q1
#2: Protein
Tsi1


Mass: 16855.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1845 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9I2Q0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 250 mM ammonium sulfate, 18% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 35069 / Num. obs: 35044 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 17
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 6.48 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXDphasing
SHELXEmodel building
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.2→49.33 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.877 / SU B: 47.993 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26309 1753 5 %RANDOM
Rwork0.22397 ---
obs0.226 33289 100 %-
all-35044 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8893 0 0 0 8893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229089
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.971.94212302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15851163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90424.299428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.124151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2711564
X-RAY DIFFRACTIONr_chiral_restr0.0640.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.23590
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.26131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2431.55883
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.33229203
X-RAY DIFFRACTIONr_scbond_it0.63633630
X-RAY DIFFRACTIONr_scangle_it0.9884.53099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1085medium positional0.340.5
12C1085medium positional0.350.5
13E1085medium positional0.320.5
14G1085medium positional0.320.5
21B1118medium positional0.410.5
22D1118medium positional0.430.5
23F1118medium positional0.430.5
24H1118medium positional0.430.5
11A1085medium thermal0.122
12C1085medium thermal0.162
13E1085medium thermal0.142
14G1085medium thermal0.132
21B1118medium thermal0.22
22D1118medium thermal0.172
23F1118medium thermal0.162
24H1118medium thermal0.182
LS refinement shellResolution: 3.199→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 125 -
Rwork0.302 2370 -
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)
13.9417-0.4171-0.46794.3231-1.30994.58930.08120.5640.8292-0.340.13380.4151-0.6197-0.6624-0.2149-0.2710.0729-0.02620.05280.22980.050586.165109.117372.5435
25.11850.81670.65884.8553-2.40343.24310.0913-0.6222-0.9076-0.1341-0.4987-0.67680.5520.3860.4074-0.30880.04410.10510.03830.3909-0.1627107.481257.874492.2421
34.6423-1.7270.44666.9-0.47273.47530.1414-0.1017-0.194-0.13660.33592.17050.0809-0.858-0.4773-0.0887-0.06470.0473-0.12160.19580.620772.950179.938132.8854
43.85410.69860.2964.4667-0.19322.1273-0.217-0.1338-1.1407-0.7099-0.1883-1.48240.56310.47490.40530.35630.11580.5697-0.2810.17550.3679126.269858.58621.6871
52.2147-0.01360.33873.71890.16783.5594-0.1379-0.27220.25860.25980.17590.2208-0.1714-0.2987-0.038-0.44010.00640.04660.01350.0264-0.335385.409390.821792.4611
63.512-1.08680.38164.7495-0.45554.2647-0.11640.111-0.3407-0.64170.10920.26340.4814-0.37940.0072-0.2997-0.1028-0.0565-0.12530.063-0.435289.481768.868675.2592
74.6196-1.0833-0.5835.5515-0.48773.89710.0934-0.745-0.38740.3902-0.02470.72440.2333-0.1764-0.06870.0158-0.06330.0949-0.29380.1401-0.305391.514762.239241.3607
83.26210.63920.23294.503-1.3493.4221-0.04280.4608-0.3608-1.49220.06250.01390.2711-0.1802-0.01970.6424-0.06570.0597-0.377-0.0639-0.3243100.23857.856814.9156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 149
2X-RAY DIFFRACTION2C4 - 149
3X-RAY DIFFRACTION3E3 - 148
4X-RAY DIFFRACTION4G4 - 148
5X-RAY DIFFRACTION5B23 - 169
6X-RAY DIFFRACTION6D23 - 169
7X-RAY DIFFRACTION7F23 - 169
8X-RAY DIFFRACTION8H23 - 168

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