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- PDB-3wa5: Crystal Structure of type VI peptidoglycan muramidase effector Ts... -

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Basic information

Entry
Database: PDB / ID: 3wa5
TitleCrystal Structure of type VI peptidoglycan muramidase effector Tse3 in complex with its cognate immunity protein Tsi3
Components
  • Tse3-specific immunity protein
  • Type VI secretion exported 3Type VI secretion system
KeywordsHYDROLASE / PROTEIN-PROTEIN COMPLEX / muramidase
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 / SAD / Resolution: 1.9 Å
AuthorsDing, J. / Wang, T. / Liu, W. / Wang, D.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein.
Authors: Wang, T. / Ding, J. / Zhang, Y. / Wang, D.C. / Liu, W.
History
DepositionApr 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type VI secretion exported 3
B: Tse3-specific immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,28813
Polymers62,6712
Non-polymers61711
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-14 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.970, 109.970, 84.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-959-

HOH

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Components

#1: Protein Type VI secretion exported 3 / Type VI secretion system


Mass: 45741.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3484 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYC5
#2: Protein Tse3-specific immunity protein


Mass: 16929.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3485 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYC4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% Jaffamine ED-2001, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→49.18 Å / Num. all: 41634 / Num. obs: 41634 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.4 % / Biso Wilson estimate: 14.59 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 28.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 28.8 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 11.8 / Num. unique all: 5971 / Rsym value: 0.335 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX(1.7.3_928)phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.18 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8827 / SU ML: 0.19 / σ(F): 0 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 2090 5.03 %RANDOM
Rwork0.1602 ---
all0.1623 41573 --
obs0.1623 41573 100 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.942 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 95.01 Å2 / Biso mean: 14.39 Å2 / Biso min: 3.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.024 Å20 Å20 Å2
2---0.024 Å2-0 Å2
3---0.048 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 35 525 4588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074135
X-RAY DIFFRACTIONf_angle_d1.0945607
X-RAY DIFFRACTIONf_dihedral_angle_d13.8941537
X-RAY DIFFRACTIONf_chiral_restr0.074620
X-RAY DIFFRACTIONf_plane_restr0.006748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.94420.21111220.16512584
1.9442-1.99280.20081250.14922608
1.9928-2.04670.21021340.15142590
2.0467-2.10690.19851340.15092615
2.1069-2.17490.22291130.15192604
2.1749-2.25270.20281240.15032606
2.2527-2.34290.18991300.15052615
2.3429-2.44950.19171340.15462613
2.4495-2.57860.20641280.1662632
2.5786-2.74020.24111640.16842611
2.7402-2.95170.22071420.16422619
2.9517-3.24870.20441720.17372619
3.2487-3.71870.21831420.16712657
3.7187-4.68450.16871670.14412668
4.6845-49.19650.19071590.17482842

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