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- PDB-4m5f: complex structure of Tse3-Tsi3 -

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Basic information

Entry
Database: PDB / ID: 4m5f
Titlecomplex structure of Tse3-Tsi3
Components(Uncharacterized protein) x 2
KeywordsHYDROLASE INHIBITOR / Beta-sheets
Function / homology
Function and homology information


host cell membrane / lysozyme / lysozyme activity / extracellular region / membrane / metal ion binding
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
PHOSPHATE ION / Immune protein Tsi3 / Peptidoglycan muramidase Tse3
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGu, L.C.
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
DepositionAug 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Derived calculations
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Nov 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9618
Polymers57,5552
Non-polymers4056
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-53 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.242, 92.242, 169.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Uncharacterized protein


Mass: 43520.977 Da / Num. of mol.: 1 / Fragment: fragment
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: 14034.423 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / pH: 7.8
Details: 0.8M Na2HPO4/KH2PO4, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26198 / % possible obs: 85 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m5e

4m5e


Resolution: 2.5→33.34 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1956 7.7 %
Rwork0.193 --
obs0.197 25394 97.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.01 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3187 Å20 Å2-0 Å2
2--5.3187 Å2-0 Å2
3----10.6374 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 18 160 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084129
X-RAY DIFFRACTIONf_angle_d1.1545622
X-RAY DIFFRACTIONf_dihedral_angle_d16.4511521
X-RAY DIFFRACTIONf_chiral_restr0.073619
X-RAY DIFFRACTIONf_plane_restr0.005748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56060.31131320.22311550X-RAY DIFFRACTION92
2.5606-2.62980.24741330.20141590X-RAY DIFFRACTION95
2.6298-2.70720.28741330.19941605X-RAY DIFFRACTION95
2.7072-2.79450.26581370.1921608X-RAY DIFFRACTION95
2.7945-2.89440.27611350.20511646X-RAY DIFFRACTION97
2.8944-3.01020.25921380.19661652X-RAY DIFFRACTION97
3.0102-3.14710.27521370.20951676X-RAY DIFFRACTION98
3.1471-3.31290.27911400.20211671X-RAY DIFFRACTION98
3.3129-3.52020.291380.19921657X-RAY DIFFRACTION97
3.5202-3.79170.24571420.19941673X-RAY DIFFRACTION98
3.7917-4.17260.21131430.17711710X-RAY DIFFRACTION98
4.1726-4.77480.20551450.15631742X-RAY DIFFRACTION100
4.7748-6.010.23921460.21251772X-RAY DIFFRACTION100
6.01-33.33770.20381570.18781886X-RAY DIFFRACTION100

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