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- PDB-4n88: Crystal structure of Tse3-Tsi3 complex with calcium ion -

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Basic information

Entry
Database: PDB / ID: 4n88
TitleCrystal structure of Tse3-Tsi3 complex with calcium ion
Components(Uncharacterized protein) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / lysozyme / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / lysozyme / lysozyme activity / extracellular region / metal ion binding / membrane
Similarity search - Function
Jelly Rolls - #1690 / : / : / T6SS, Peptidoglycan muramidase Tse3, catalytic domain / T6SS, Peptidoglycan muramidase Tse3, N-terminal domain / : / : / Type six secretion immunity 3 domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls ...Jelly Rolls - #1690 / : / : / T6SS, Peptidoglycan muramidase Tse3, catalytic domain / T6SS, Peptidoglycan muramidase Tse3, N-terminal domain / : / : / Type six secretion immunity 3 domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShang, G.J.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex from Pseudomonas aeruginosa reveal a calcium-dependent membrane-binding mechanism
Authors: Lu, D. / Shang, G. / Zhang, H. / Yu, Q. / Cong, X. / Yuan, J. / He, F. / Zhu, C. / Zhao, Y. / Yin, K. / Chen, Y. / Hu, J. / Zhang, X. / Yuan, Z. / Xu, S. / Hu, W. / Cang, H. / Gu, L.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Nov 8, 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 / database_2 / pdbx_initial_refinement_model / 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_conn.ptnr2_label_seq_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

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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)114,82512
Polymers114,5044
Non-polymers3218
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4126
Polymers57,2522
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-0 kcal/mol
Surface area23160 Å2
MethodPISA
3
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4126
Polymers57,2522
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint0 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.236, 95.317, 160.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 43618.031 Da / Num. of mol.: 2 / Fragment: UNP residues 2-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3484 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC5
#2: Protein Uncharacterized protein


Mass: 13634.102 Da / Num. of mol.: 2 / Fragment: UNP residues 27-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3485 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.2M Ammonium acetate, 0.01M calcium chloride,0.05M Sodium cacodylate pH 6.5, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 34326 / % possible obs: 99.9 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7S

4n7s


Resolution: 2.8→41.384 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 27.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2688 1681 5.05 %
Rwork0.2017 --
obs0.205 33266 96.31 %
all-34326 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.596 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2956 Å20 Å2-0 Å2
2--16.8288 Å2-0 Å2
3----15.5332 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8028 0 8 99 8135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098216
X-RAY DIFFRACTIONf_angle_d1.15611186
X-RAY DIFFRACTIONf_dihedral_angle_d15.883048
X-RAY DIFFRACTIONf_chiral_restr0.0741236
X-RAY DIFFRACTIONf_plane_restr0.0051494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.798-2.88040.35921130.26252257X-RAY DIFFRACTION83
2.8804-2.97340.33381460.25732465X-RAY DIFFRACTION92
2.9734-3.07960.38241330.25232519X-RAY DIFFRACTION94
3.0796-3.20290.3491450.25172575X-RAY DIFFRACTION96
3.2029-3.34860.30681370.24352642X-RAY DIFFRACTION97
3.3486-3.5250.28771500.23372639X-RAY DIFFRACTION97
3.525-3.74580.27211520.21932659X-RAY DIFFRACTION99
3.7458-4.03470.26591450.18732665X-RAY DIFFRACTION98
4.0347-4.44040.23391360.16582721X-RAY DIFFRACTION99
4.4404-5.08190.23231370.17412748X-RAY DIFFRACTION99
5.0819-6.39880.25851490.20342791X-RAY DIFFRACTION100
6.3988-41.38890.20821380.16342904X-RAY DIFFRACTION99

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