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- PDB-5h7z: Apo structure of immunity protein TplEi of T6SS from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 5h7z
TitleApo structure of immunity protein TplEi of T6SS from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsHYDROLASE INHIBITOR / antimicrobial peptide / effector -immunity complex / inhibitor
Function / homologyTle cognate immunity protein 4, N-terminal domain / Tle cognate immunity protein 4 N-terminal domain / Tle cognate immunity protein 4, C-terminal domain / Tle cognate immunity protein 4 C-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tle cognate immunity protein 4 C-terminal domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.057 Å
AuthorsGao, X.P. / Mu, Z.X. / Cui, S.
Funding support China, 3items
OrganizationGrant numberCountry
Beijing Natural Science Foundation7154226 China
National Natural Science Foundation of China81401714 China
CitationJournal: Front Cell Infect Microbiol / Year: 2017
Title: Structure-Based Prototype Peptides Targeting the Pseudomonas aeruginosa Type VI Secretion System Effector as a Novel Antibacterial Strategy
Authors: Gao, X.P. / Mu, Z.X. / Qin, B. / Sun, Y. / Cui, S.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78314
Polymers84,6302
Non-polymers1,15312
Water00
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9888
Polymers42,3151
Non-polymers6727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7956
Polymers42,3151
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.227, 182.227, 78.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Uncharacterized protein


Mass: 42315.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA1509 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9I3K3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
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: 3.87 Å3/Da / Density % sol: 68.2 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.52M LI2SO4, 13% peg8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97876 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationMonochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 3.057→31.252 Å / Num. obs: 46474 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.28 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.44
Reflection shellResolution: 3.06→3.24 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.67 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.057→31.252 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2448 2380 5.12 %
Rwork0.2031 --
obs0.2053 46450 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.057→31.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 60 0 4834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034989
X-RAY DIFFRACTIONf_angle_d0.8726761
X-RAY DIFFRACTIONf_dihedral_angle_d15.041835
X-RAY DIFFRACTIONf_chiral_restr0.051702
X-RAY DIFFRACTIONf_plane_restr0.004873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0569-3.11920.3105810.33081307X-RAY DIFFRACTION49
3.1192-3.1870.34021320.30122653X-RAY DIFFRACTION100
3.187-3.26110.32011690.30012674X-RAY DIFFRACTION100
3.2611-3.34250.35521710.26972634X-RAY DIFFRACTION100
3.3425-3.43280.29771230.2552735X-RAY DIFFRACTION100
3.4328-3.53370.28971410.23672628X-RAY DIFFRACTION100
3.5337-3.64760.30731520.23012706X-RAY DIFFRACTION100
3.6476-3.77770.28991460.21012675X-RAY DIFFRACTION100
3.7777-3.92870.26881110.20922683X-RAY DIFFRACTION100
3.9287-4.10710.24881530.20822670X-RAY DIFFRACTION100
4.1071-4.32310.22661230.18692702X-RAY DIFFRACTION100
4.3231-4.59320.20451630.16792650X-RAY DIFFRACTION100
4.5932-4.94660.20221520.15232681X-RAY DIFFRACTION100
4.9466-5.4420.19221310.17012670X-RAY DIFFRACTION100
5.442-6.22410.2071560.18272691X-RAY DIFFRACTION100
6.2241-7.82130.19911280.21012675X-RAY DIFFRACTION100
7.8213-31.25330.21721480.16782636X-RAY DIFFRACTION98

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