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- PDB-7uma: Crystal structure of Tlde1a from Salmonella Typhimurium -

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Basic information

Entry
Database: PDB / ID: 7uma
TitleCrystal structure of Tlde1a from Salmonella Typhimurium
Components
  • HIS-HIS-HIS-HIS
  • Tlde1a
KeywordsTOXIN / Type VI secretion system / Salmonella Typhimurium / L / D-carboxypeptidase / D-transpeptidase / peptidoglycan
Function / homologyDUF2778 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsLorente Cobo, N. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Molecular characterization of the type VI secretion system effector Tlde1a reveals a structurally altered LD-transpeptidase fold.
Authors: Lorente Cobo, N. / Sibinelli-Sousa, S. / Biboy, J. / Vollmer, W. / Bayer-Santos, E. / Prehna, G.
History
DepositionApr 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Refinement description / Category: refine
Item: _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tlde1a
C: HIS-HIS-HIS-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8997
Polymers20,4192
Non-polymers4805
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-85 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.381, 59.381, 105.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

21A-518-

HOH

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Components

#1: Protein Tlde1a / Murein L / D-transpeptidase / SciV protein


Mass: 19442.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct has a His-tag at the carboxy-terminus, but the tag interacts with the active site of a symmetry-related copy of the protein.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sciV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: H9L4J5
#2: Protein/peptide HIS-HIS-HIS-HIS


Mass: 976.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His-tag from a symmetry-related copy of the Tlde1a construct
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 12mg/ml Tlde1a, 15% PEG 3350, 0.2M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→41.99 Å / Num. obs: 25343 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Net I/σ(I): 25.9
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1118 / CC1/2: 0.525 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: NaI derivative solved using SAD

Resolution: 1.6→29.69 Å / SU ML: 0.1508 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.0814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1873 1227 4.85 %
Rwork0.165 24048 -
obs0.1661 25275 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 25 232 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091464
X-RAY DIFFRACTIONf_angle_d0.93381984
X-RAY DIFFRACTIONf_chiral_restr0.0646195
X-RAY DIFFRACTIONf_plane_restr0.0088256
X-RAY DIFFRACTIONf_dihedral_angle_d13.5863525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.27871230.24072546X-RAY DIFFRACTION97.73
1.67-1.740.24211250.1852653X-RAY DIFFRACTION100
1.74-1.840.18021520.17192589X-RAY DIFFRACTION100
1.84-1.950.19821250.16612664X-RAY DIFFRACTION100
1.95-2.10.19331430.15582642X-RAY DIFFRACTION100
2.1-2.310.16021410.14952646X-RAY DIFFRACTION99.96
2.31-2.650.1811270.15912709X-RAY DIFFRACTION100
2.65-3.340.19151280.16262729X-RAY DIFFRACTION100
3.34-29.690.17981630.16522870X-RAY DIFFRACTION99.93
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)
12.385670561393.628748711082.481661172747.365145114142.063398492495.734092247510.0591423863667-0.2915665787840.1590639230.0800056807193-0.05716341161310.129925237255-0.150566265892-0.06633182621670.00749879103660.08360482168960.01825956822240.02206938060630.129132544369-0.02507916167860.074808604219611.606926945724.401021662444.5610013578
22.195843910471.657692260371.12178181836.631874213912.468374144563.37975405741-0.0988765305189-0.0007797511618990.13810397776-0.2064804228260.03138648874750.328133259379-0.135442310313-0.1645924107330.07360793924720.05536034717820.0233677438313-0.0006348402157960.1228004872090.007181395564710.07119246866676.0973852529720.963639526537.7350866142
37.668764309120.805747820792-1.408970260428.140967471092.200716457372.164006399310.114651399112-0.0964690801861-0.6071189369510.0252850440215-0.0627328695507-0.03673315461090.145751778249-0.307425267303-0.09067490876150.105576066485-0.00941861998947-0.02314317447220.1030735498330.02604246051020.1587674787849.569595441829.2821061782236.8680372434
41.697204519940.875287799260.09502347263368.49810482017-5.981334294946.25759705109-0.0564810174860.2548944972970.01287696650010.141163721398-0.0711825656365-0.419476918764-0.3160910657820.4568706123120.1377975439820.101343376056-0.0431538747396-0.0008131237250610.18324265057-0.01215438765640.13180880955723.650679661424.014497341436.9796717471
59.47658011696.517205490866.028954026365.281831877695.076942310764.919805111130.1408819901551.26765272235-0.63218827704-0.5846507269840.281650691268-0.5898246320190.1540739282391.32358728378-0.2763016360190.5108469379390.003881894622370.02013770827540.65435993772-0.02784438029680.20338933460622.528407261721.181515084817.3136094509
63.238160152240.1267293226232.347820194711.79515079245-1.265287814385.48850582002-0.12377199960.7982772374840.0566611018917-0.3193329326830.142271312886-0.01974220016510.06100137780080.68193360180.03578929230810.173153298283-0.06141947247150.01759014793150.3146621099620.01659297288090.13042962615919.98256105824.818315962222.396325245
72.131717053410.7611711054551.55169302731.811823962922.540503076746.37425215032-0.171518770330.6581198199810.194366569041-0.5410445924170.113724157545-0.0739559215704-0.4782849634340.2650894652920.01672855275510.220151727508-0.06371948611280.00224130162570.2831742332130.05253829040190.1239798279811.762102173523.323597683618.9580062998
82.983378917260.01113852624871.119416761393.53876245816-1.365667568583.744380334610.08913481266410.0480148099177-0.502490874479-0.03324418333990.0631286209057-0.07762048934240.3268253080170.218950760821-0.1168331203020.09711861540160.0246905031665-0.002140860776230.114883091638-0.01172498454390.17227069130419.904163668914.290117210136.2594047229
95.270203208334.267463010962.852896141326.8354109523.349711979994.99319358466-0.1741872228160.09399954986810.309417576456-0.1873876777130.03221698094960.0175172430592-0.40177554280.05869898598420.1365660249490.108184494943-0.002723499245460.0009632937593440.1204734362310.02589300174630.099661532354512.025127722228.392334546933.3239508007
105.380944120982.523544540490.3404755389936.85034460385-0.6563777160222.601060486290.062071526796-0.1911627435360.441765622420.467675229621-0.122172119397-0.726527944873-0.6433121324670.479448174045-0.003305306411720.219541055008-0.0924922052856-0.02919538280150.241138277916-0.03109431552910.23769420744423.914654394631.164606942542.6029779094
117.8751859794-1.714455113522.513820017162.69744526232-2.908082073547.38223411395-0.0306215617002-0.4486159258890.2155147723530.1873598325840.04353213193630.118196480362-0.145200801743-0.341648579044-0.07019887283910.0990191901637-0.0119389413348-0.002635663136560.159789073728-0.04904628373860.1122004615632.6792323216719.610895197638.8103418479
124.89308932911-4.836504153982.899956332648.40284355399-5.582313410893.751775263620.746621404852.12566028701-0.00987343595999-1.64309316213-0.490560892486-0.0637158128661.440488615190.626106957509-0.207343751381.20080868222-0.09290580113330.01904304405860.731893774846-0.07129306517720.44699740598416.792235157613.582993532923.9465912387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 15 )AA3 - 151 - 13
22chain 'A' and (resid 16 through 32 )AA16 - 3214 - 30
33chain 'A' and (resid 33 through 45 )AA33 - 4531 - 43
44chain 'A' and (resid 46 through 55 )AA46 - 5544 - 53
55chain 'A' and (resid 56 through 65 )AA56 - 6554 - 63
66chain 'A' and (resid 66 through 83 )AA66 - 8364 - 81
77chain 'A' and (resid 84 through 95 )AA84 - 9582 - 93
88chain 'A' and (resid 96 through 121 )AA96 - 12194 - 119
99chain 'A' and (resid 122 through 146 )AA122 - 146120 - 144
1010chain 'A' and (resid 147 through 159 )AA147 - 159145 - 157
1111chain 'A' and (resid 160 through 174 )AA160 - 174158 - 172
1212chain 'C' and (resid 301 through 304 )CG301 - 3041 - 4

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