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- PDB-4luq: Crystal structure of virulence effector Tse3 in complex with neut... -

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Basic information

Entry
Database: PDB / ID: 4luq
TitleCrystal structure of virulence effector Tse3 in complex with neutralizer Tsi3
Components(Uncharacterized protein) x 2
KeywordsPROTEIN BINDING/TOXIN INHIBITOR / goose type lysozyme / catalytic domain / ARM / HEAT like motif / muramidase / Tsi3 / PROTEIN BINDING-TOXIN INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / lysozyme / lysozyme activity / extracellular region / membrane / metal ion binding
Similarity search - Function
Jelly Rolls - #1690 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immune protein Tsi3 / Peptidoglycan muramidase Tse3
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.77 Å
AuthorsWang, T. / Li, L. / Zhang, W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Insights on the Bacteriolytic and Self-protection Mechanism of Muramidase Effector Tse3 in Pseudomonas aeruginosa
Authors: Li, L. / Zhang, W. / Liu, Q. / Gao, Y. / Gao, Y. / Wang, Y. / Wang, D.Z. / Li, Z. / Wang, T.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Jul 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,36610
Polymers125,1264
Non-polymers2406
Water13,781765
1
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6835
Polymers62,5632
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6835
Polymers62,5632
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized protein
hetero molecules

C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,6835
Polymers62,5632
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2090 Å2
ΔGint-35 kcal/mol
Surface area22900 Å2
MethodPISA
4
B: Uncharacterized protein
hetero molecules

D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,6835
Polymers62,5632
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2110 Å2
ΔGint-35 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.333, 81.288, 111.414
Angle α, β, γ (deg.)90.00, 93.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.990719, -0.011264, 0.135459), (-0.011884, -0.999922, 0.003763), (0.135407, -0.005338, -0.990776)3.56977, 5.92802, -55.5136

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Components

#1: Protein Uncharacterized protein / virulence effector Tse3


Mass: 46607.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3484 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9HYC5
#2: Protein Uncharacterized protein / antitoxin Tsi3


Mass: 15955.582 Da / Num. of mol.: 2 / Fragment: UNP residues 23-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3485 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9HYC4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.2
Details: 100mM HEPES, 2M NH4COOH, 50uM CaCl2, pH 7.2, VAPOR DIFFUSION, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-002+11.5418
SYNCHROTRONSSRF BL17U20.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDOct 10, 2012
RIGAKU SATURN 944+2CCDOct 30, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2sealed tube with micro focusSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97911
ReflectionResolution: 1.77→50 Å / Num. all: 109985 / Num. obs: 109546 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 17.95 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.053 / Net I/σ(I): 25.44
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.77-1.83.70.2536.881,299.7
1.8-1.833.70.228.271,2100
3.81-4.83.40.0421061,298
4.8-503.60.038101.21,296.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.77→40.52 Å
RfactorNum. reflection
Rfree0.188 5484
Rwork0.139 -
all-104041
obs-101612
Displacement parametersBiso mean: 25.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20.16 Å2
2---0.55 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.77→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8226 0 6 765 8997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198407
X-RAY DIFFRACTIONr_bond_other_d0.0010.027961
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.96311441
X-RAY DIFFRACTIONr_angle_other_deg0.943318259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9751063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64923.41393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.048151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2951582
X-RAY DIFFRACTIONr_chiral_restr0.1210.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021963
X-RAY DIFFRACTIONr_rigid_bond_restr7.127316368
X-RAY DIFFRACTIONr_sphericity_free18.7365266
X-RAY DIFFRACTIONr_sphericity_bonded7.18516692
LS refinement shellResolution: 1.767→1.813 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 427 -
Rwork0.133 7316 -
obs--94.79 %
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)
11.4589-0.6747-0.62121.24040.66071.48290.0356-0.01670.03810.034-0.06190.0811-0.0059-0.14150.02630.0167-0.0198-0.00050.04090.00060.015-0.083910.9017-43.1553
21.21980.60740.60131.29020.72521.68020.02550.0266-0.01460.0233-0.06170.08520.0776-0.13510.03620.07120.02340.00680.0349-0.00210.0114-2.0055-4.9977-12.722
35.3141.0953-1.18561.216-0.881.4639-0.08680.3658-0.0945-0.0926-0.0531-0.3461-0.04670.41540.13990.0676-0.05720.02110.27610.00490.1425-27.880111.9761-60.1182
45.0089-0.99751.98932.7962-1.21162.2355-0.1092-0.2967-0.05470.3838-0.1158-0.8791-0.08850.4320.2250.19660.0185-0.13280.2670.05310.3074-31.6051-5.86198.0013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 408
2X-RAY DIFFRACTION2B0 - 408
3X-RAY DIFFRACTION3C23 - 145
4X-RAY DIFFRACTION4D20 - 145

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