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- PDB-4f0w: Crystal structure of type effector Tse1 C30A mutant from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 4f0w
TitleCrystal structure of type effector Tse1 C30A mutant from Pseudomonas aeruginousa
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / NlpC/P60 domain
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
MALONATE ION / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa.
Authors: Zhang, H. / Gao, Z.Q. / Su, X.D. / Dong, Y.H.
History
DepositionMay 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Apr 3, 2024Group: 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 / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3593
Polymers20,1651
Non-polymers1942
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.432, 62.305, 73.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / effector Tse1


Mass: 20164.676 Da / Num. of mol.: 1 / Mutation: C30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2Q1
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Sodium malonate pH 7.0, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. all: 48208 / Num. obs: 48208 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 27.8
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.47 / Num. unique all: 2300 / % possible all: 92.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native paTse1 structure

Resolution: 1.24→29.887 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 16.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2439 5.06 %RANDOM
Rwork0.1828 ---
all0.1833 48208 --
obs0.1833 48159 94.79 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.804 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6448 Å20 Å2-0 Å2
2--1.4577 Å20 Å2
3----0.8128 Å2
Refinement stepCycle: LAST / Resolution: 1.24→29.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 13 235 1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071210
X-RAY DIFFRACTIONf_angle_d1.1081646
X-RAY DIFFRACTIONf_dihedral_angle_d13.43452
X-RAY DIFFRACTIONf_chiral_restr0.068177
X-RAY DIFFRACTIONf_plane_restr0.004216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2401-1.26540.30091240.2616262294
1.2654-1.29290.23691500.2387264395
1.2929-1.3230.25051590.2233266295
1.323-1.3560.20321670.2112263595
1.356-1.39270.19751410.1956267996
1.3927-1.43370.19221510.1884272597
1.4337-1.480.17981240.1834273096
1.48-1.53280.21251320.1735270897
1.5328-1.59420.17721400.167274496
1.5942-1.66680.18661560.1632270196
1.6668-1.75460.18681570.1663268596
1.7546-1.86460.16751230.1678273196
1.8646-2.00850.18341310.1775273995
2.0085-2.21060.18281560.1771269395
2.2106-2.53030.19541340.1862268493
2.5303-3.18730.21231430.1893265391
3.1873-29.89610.17261510.1769268689
Refinement TLS params.Method: refined / Origin x: 0.2085 Å / Origin y: 18.7054 Å / Origin z: 13.3183 Å
111213212223313233
T0.0119 Å20.0019 Å20.0003 Å2-0.0161 Å20.0079 Å2--0.012 Å2
L0.5898 °2-0.026 °2-0.178 °2-0.7191 °20.1436 °2--0.722 °2
S0.0068 Å °-0.0754 Å °0.0013 Å °0.0658 Å °0.0145 Å °-0.0295 Å °0.0132 Å °0.0272 Å °-0.013 Å °
Refinement TLS groupSelection details: ALL

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