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- PDB-5jkp: Crystal structure of immunity protein Pa5087 from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 5jkp
TitleCrystal structure of immunity protein Pa5087 from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsIMMUNE SYSTEM / immunity protein
Function / homologySel1-like repeat / Sel1-like repeats. / : / Tetratricopeptide-like helical domain superfamily / protein ubiquitination / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.106 Å
AuthorsLi, Z.Q. / Gao, Z.Q. / She, Z. / Dong, Y.H.
CitationJournal: Febs Lett. / Year: 2016
Title: Structural analysis of Pseudomonas aeruginosa H3-T6SS immunity proteins
Authors: Yang, X.Y. / Li, Z.Q. / She, Z. / Geng, Z. / Xu, J.H. / Gao, Z.Q. / Dong, Y.H.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)30,2201
Polymers30,2201
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13920 Å2
Unit cell
Length a, b, c (Å)58.015, 58.686, 78.720
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 Uncharacterized protein


Mass: 30220.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA5087 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HU96
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Calcium acetate, 0.1M MES, 15% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16110 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.97 / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.56
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.22 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JJO

5jjo


Resolution: 2.106→27.495 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 804 5.01 %random selection
Rwork0.196 ---
obs0.1981 16056 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.106→27.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 135 2227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032161
X-RAY DIFFRACTIONf_angle_d0.672946
X-RAY DIFFRACTIONf_dihedral_angle_d12.0181288
X-RAY DIFFRACTIONf_chiral_restr0.044298
X-RAY DIFFRACTIONf_plane_restr0.006385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1063-2.23830.26531340.20952496X-RAY DIFFRACTION100
2.2383-2.4110.24981280.22972494X-RAY DIFFRACTION100
2.411-2.65340.27221520.21442511X-RAY DIFFRACTION100
2.6534-3.0370.28011350.22612507X-RAY DIFFRACTION100
3.037-3.82460.24121280.20042556X-RAY DIFFRACTION100
3.8246-27.49730.19841270.16692688X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.1207 Å / Origin y: -10.4724 Å / Origin z: 74.4852 Å
111213212223313233
T0.1698 Å20.0218 Å20.0105 Å2-0.2392 Å2-0.0149 Å2--0.2102 Å2
L0.6875 °20.6517 °2-0.3078 °2-1.7399 °2-0.6374 °2--0.7219 °2
S0.0046 Å °-0.0314 Å °0.037 Å °0.0132 Å °-0.0246 Å °0.0399 Å °0.0125 Å °-0.0027 Å °0.0014 Å °
Refinement TLS groupSelection details: all

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