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- PDB-4fqa: Crystal structure of toxic effector Tse1 -

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Basic information

Entry
Database: PDB / ID: 4fqa
TitleCrystal structure of toxic effector Tse1
Componentstoxic effector Tse1
KeywordsTOXIN / helix and strand / toxic effector / Tsi1
Function / homology
Function and homology information


gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane
Similarity search - Function
endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsLi, L. / Zhang, W. / Wang, T.
CitationJournal: To be Published
Title: Structural insight on toxic effector Tse1
Authors: Li, L. / Zhang, W. / Wang, T.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: toxic effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,5301
Polymers17,5301
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.640, 61.460, 64.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer binds with Tsi1

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Components

#1: Protein toxic effector Tse1


Mass: 17529.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6His-tagged / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1844 / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.3
Details: 100mM Tris, 25%PEG3350, mM DTT, pH 8.3, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-002+11.5418
ROTATING ANODERIGAKU MICROMAX-002+21.5418
Detector
TypeIDDetectorDate
RIGAKU SATURN 944+1CCDSep 15, 2011
RIGAKU SATURN 944+2CCDOct 14, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 12272 / Num. obs: 11866 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 15.75 Å2 / Rmerge(I) obs: 0.118
Reflection shellResolution: 2.14→2.25 Å / Redundancy: 6.24 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1206 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
REFMAC5.6.0117refinement
CrystalCleardata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.077 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22833 394 4.7 %RANDOM
Rwork0.18084 ---
obs0.18308 7974 91.27 %-
all-8366 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.881 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---0.43 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 0 120 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191194
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9421619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9324.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63115190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.647157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021913
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 24 -
Rwork0.18 559 -
obs--99.49 %
Refinement TLS params.Method: refined / Origin x: 13.5179 Å / Origin y: -0.0255 Å / Origin z: -1.0266 Å
111213212223313233
T0.0313 Å20.0097 Å2-0.0084 Å2-0.0068 Å2-0.007 Å2--0.0338 Å2
L1.6544 °20.0941 °2-0.1564 °2-2.822 °2-0.2802 °2--4.5849 °2
S-0.0195 Å °-0.0151 Å °-0.1309 Å °-0.0185 Å °0.0504 Å °-0.0815 Å °0.3669 Å °0.0947 Å °-0.0309 Å °

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