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- PDB-3vpi: Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3vpi
TitleCrystal structure of type VI effector Tse1 from Pseudomonas aeruginosa
Componentstype VI secretion exported 1
KeywordsHYDROLASE
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
FORMIC ACID / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsDing, J. / Wang, W. / Wang, D.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural insights into the Pseudomonas aeruginosa type VI virulence effector Tse1 bacteriolysis and self-protection mechanisms
Authors: Ding, J. / Wang, W. / Feng, H. / Zhang, Y. / Wang, D.C.
History
DepositionMar 4, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: type VI secretion exported 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,27910
Polymers18,8651
Non-polymers4149
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.450, 63.640, 73.740
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 type VI secretion exported 1


Mass: 18864.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1844 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.8M sodium formate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONBSRF 3W1A20.9795
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDNov 14, 2011
ADSC QUANTUM 210r2CCDNov 26, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
ReflectionResolution: 1.5→26.61 Å / Num. all: 29556 / Num. obs: 29544 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 4.8 / Num. unique all: 4061 / Rsym value: 0.266 / % possible all: 96

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→26.61 Å / FOM work R set: 0.9023 / SU ML: 0.12 / σ(F): 0 / Phase error: 16.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1474 5.08 %RANDOM
Rwork0.1647 ---
obs0.1657 29040 97.74 %-
all-29544 --
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.59 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso mean: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.4692 Å2-0 Å2-0 Å2
2---0.6065 Å20 Å2
3----0.8627 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.5→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 27 264 1426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151216
X-RAY DIFFRACTIONf_angle_d1.0111580
X-RAY DIFFRACTIONf_dihedral_angle_d11.412416
X-RAY DIFFRACTIONf_chiral_restr0.066169
X-RAY DIFFRACTIONf_plane_restr0.003204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.54840.20391230.1866222588
1.5484-1.60380.19661190.1761244696
1.6038-1.6680.17871190.1671247098
1.668-1.74390.21731370.1622247698
1.7439-1.83580.1811210.1569254299
1.8358-1.95080.1961280.1736246898
1.9508-2.10130.16981240.1604253599
2.1013-2.31270.18941370.1655255099
2.3127-2.64710.1881580.16892546100
2.6471-3.3340.17481500.16262602100
3.334-26.61620.17531580.15942706100

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