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- PDB-4eqa: Crystal structure of PA1844 in complex with PA1845 from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 4eqa
TitleCrystal structure of PA1844 in complex with PA1845 from Pseudomonas aeruginosa PAO1
Components(Putative uncharacterized protein) x 2
KeywordsUNKNOWN FUNCTION / TYPE VI SECRETION / T6S / ANTITOXIN-TOXIN complex
Function / homology
Function and homology information


gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane
Similarity search - Function
Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Lipocalin / Alpha-Beta Complex / Beta Barrel ...Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Lipocalin / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immune protein Tsi1 / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShang, G. / Li, N. / Zhang, J. / Lu, D. / Yu, Q. / Zhao, Y. / Liu, X. / Xu, S. / Gu, L.
CitationJournal: Biochem.J. / Year: 2012
Title: Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.
Authors: Shang, G. / Liu, X. / Lu, D. / Zhang, J. / Li, N. / Zhu, C. / Liu, S. / Yu, Q. / Zhao, Y. / Zhang, H. / Hu, J. / Cang, H. / Xu, S. / Gu, L.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)64,9934
Polymers64,9934
Non-polymers00
Water14,034779
1
A: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,4962
Polymers32,4962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-4 kcal/mol
Surface area13400 Å2
MethodPISA
2
B: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,4962
Polymers32,4962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-4 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.514, 99.204, 56.333
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / PA1844 protein


Mass: 15640.782 Da / Num. of mol.: 2 / Fragment: The trunction, UNP residues 6-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1
#2: Protein Putative uncharacterized protein / PA1845 protein


Mass: 16855.641 Da / Num. of mol.: 2 / Fragment: The trunction, UNP residues 20-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1845 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2(DE3) / References: UniProt: Q9I2Q0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 68954 / Num. obs: 68954 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 18.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 7.9 / Num. unique all: 6876 / Rsym value: 0.364 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQ8

4eq8


Resolution: 1.6→27.22 Å / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1967 2.9 %RANDOM
Rwork0.1739 ---
all0.1748 68954 --
obs0.1748 67828 97.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.564 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8355 Å2-0 Å2-4.8205 Å2
2---3.0947 Å20 Å2
3---0.2592 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 0 779 5275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064665
X-RAY DIFFRACTIONf_angle_d0.9796314
X-RAY DIFFRACTIONf_dihedral_angle_d11.821714
X-RAY DIFFRACTIONf_chiral_restr0.068664
X-RAY DIFFRACTIONf_plane_restr0.005842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5995-1.63950.26141260.2126433591
1.6395-1.68380.27341390.2031460496
1.6838-1.73330.21021370.1884467497
1.7333-1.78930.23991390.1832461697
1.7893-1.85320.25561400.1883472898
1.8532-1.92740.24121430.1875472098
1.9274-2.01510.23651440.1851476499
2.0151-2.12130.22261420.19014769100
2.1213-2.25410.23031430.1813477499
2.2541-2.4280.20611430.18174806100
2.428-2.67220.24651440.1824803100
2.6722-3.05840.24031440.17914801100
3.0584-3.85150.14941440.15774820100
3.8515-27.22450.16961390.1519464795
Refinement TLS params.Method: refined / Origin x: -11.2997 Å / Origin y: 24.3289 Å / Origin z: -15.2746 Å
111213212223313233
T0.0877 Å2-0.003 Å2-0.007 Å2-0.0847 Å20.0042 Å2--0.0958 Å2
L0.6273 °2-0.0186 °20.1819 °2-0.6258 °2-0.0645 °2--0.4633 °2
S0.0008 Å °0.0408 Å °-0.0098 Å °-0.0976 Å °-0.0251 Å °0.1036 Å °0.0176 Å °0.0313 Å °0.0191 Å °
Refinement TLS groupSelection details: ALL

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