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- PDB-4ps2: Structure of the C-terminal fragment (87-165) of E.coli EAEC TssB... -

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Basic information

Entry
Database: PDB / ID: 4ps2
TitleStructure of the C-terminal fragment (87-165) of E.coli EAEC TssB molecule
ComponentsPutative type VI secretion protein
KeywordsCONTRACTILE PROTEIN / helices bundle / T6SS contractile sheath / TssC
Function / homologyType VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / metal ion binding / Type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDouzi, B. / Logger, L. / Spinelli, S. / Blangy, S. / Cambillau, C. / Cascales, E.
CitationJournal: To be Published
Title: Mapping the tube-sheath interface within the Type VI secretion system tail
Authors: Douzi, B. / Logger, L. / Spinelli, S. / Blangy, S. / Cambillau, C. / Cascales, E.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3813
Polymers9,2801
Non-polymers1012
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative type VI secretion protein
hetero molecules

A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7616
Polymers18,5602
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area1880 Å2
ΔGint-58 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.640, 69.150, 45.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative type VI secretion protein


Mass: 9279.812 Da / Num. of mol.: 1 / Fragment: UNP residues 88-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 042 / EAEC / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3GU37
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Zinc acetate 0.2 M, PEG3350 20%, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2013
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2→42 Å / Num. obs: 5921 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 28.11 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2 / Num. unique all: 1730 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
SHELXSphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→41.88 Å / Cor.coef. Fo:Fc: 0.9277 / Cor.coef. Fo:Fc free: 0.9224 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 568 9.61 %RANDOM
Rwork0.1809 ---
all0.1847 5913 --
obs0.1847 5913 99.92 %-
Displacement parametersBiso mean: 33.49 Å2
Baniso -1Baniso -2Baniso -3
1--8.0435 Å20 Å20 Å2
2--11.72 Å20 Å2
3----3.6765 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 2→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 2 84 725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01639HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.97864HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0237SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes017HARMONIC2
X-RAY DIFFRACTIONt_gen_planes091HARMONIC5
X-RAY DIFFRACTIONt_it0639HARMONIC20
X-RAY DIFFRACTIONt_nbd00SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion15.32
X-RAY DIFFRACTIONt_chiral_improper_torsion086SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact0828SEMIHARMONIC4
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2082 133 8.12 %
Rwork0.1841 1505 -
all0.1861 1638 -
obs--99.92 %
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)
10.0491-0.1447-0.01780.0583-0.05040.02660.0002-0.0041-0.00340.00250.00070.0045-0.0035-0.002-0.00090.00140.00420.0041-0.0150.00040.01267.447332.8322.1026
20-0.08640.15340.0272-0.08880.08750.0007-0.00160.00290.00070.0020-0.00110.0073-0.00270.0111-0.0172-0.0151-0.00050.0411-0.013517.337935.90356.7293
30.0748-0.09860.33170.1274-0.19380.00410.0007-0.00830.00960.00280.00570.00460.0043-0.0086-0.0064-0.01620.006-0.0210.00140.0190.00937.884217.1467-2.4363
40.188-0.0967-0.12120.2033-0.03790.1950.0012-0.01120.0061-0.0080.0048-0.00170.0134-0.0021-0.006-0.002-0.00470.0009-0.00450.00650.005916.00610.8196-1.7868
50.0009-0.08630.33480.0948-0.27560.1629-0.0022-0.007-0.00240.00340.0051-0.00250.0096-0.0071-0.00290.0118-0.0063-0.0104-0.00580.0131-0.014111.71412.87087.5785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|88 - A|97}A88 - 97
2X-RAY DIFFRACTION2{A|98 - A|110}A98 - 110
3X-RAY DIFFRACTION3{A|111 - A|130}A111 - 130
4X-RAY DIFFRACTION4{A|131 - A|148}A131 - 148
5X-RAY DIFFRACTION5{A|149 - A|165}A149 - 165

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