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- PDB-5czy: Crystal structure of LegAS4 -

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Basic information

Entry
Database: PDB / ID: 5czy
TitleCrystal structure of LegAS4
ComponentsLegionella effector LegAS4
KeywordsTRANSFERASE / SET domain
Function / homology
Function and homology information


LegAS4-like, SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats ...LegAS4-like, SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Eukaryotic huntingtin interacting protein B
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
Model detailscomplexed with PL-74
AuthorsSon, J. / Hwang, K.Y. / Lee, W.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of Legionella pneumophila type IV secretion system effector LegAS4
Authors: Son, J. / Jo, C.H. / Murugan, R.N. / Bang, J.K. / Hwang, K.Y. / Lee, W.C.
History
DepositionAug 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _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: Legionella effector LegAS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2085
Polymers55,5331
Non-polymers6754
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-1 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.249, 69.249, 200.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

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Components

#1: Protein Legionella effector LegAS4 / LegAS4 / Eukaryotic huntingtin interacting protein B


Mass: 55533.492 Da / Num. of mol.: 1 / Fragment: UNP residues 63-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: legAS4 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZUS4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Fragment: solvent / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Fragment: substrate / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium citrate, 15 % (v/v) isopropanol, 10%(w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→66.832 Å / Num. obs: 28465 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.21 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.071 / Χ2: 0.977 / Net I/σ(I): 29.36 / Num. measured all: 490905
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.330.9230.5483.2929661465040130.5986.3
2.33-2.490.9680.3326.5946111438442460.34996.9
2.49-2.690.9920.22112.9770933406640650.227100
2.69-2.950.9980.13823.1482686376437640.142100
2.95-3.30.9990.08436.5875125343634360.086100
3.3-3.810.9990.06149.9765574304930380.06399.6
3.81-4.660.9990.04863.4755513261126110.049100
4.66-6.570.9990.04763.3142590205920590.048100
6.5710.04165.7822712123812330.04299.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementStarting model: SAD

Resolution: 2.2→66.832 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 1443 5.08 %
Rwork0.2024 --
obs0.2046 28400 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→66.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 45 239 3927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013760
X-RAY DIFFRACTIONf_angle_d1.1225081
X-RAY DIFFRACTIONf_dihedral_angle_d15.5261399
X-RAY DIFFRACTIONf_chiral_restr0.047552
X-RAY DIFFRACTIONf_plane_restr0.005658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.27860.46841150.46432239X-RAY DIFFRACTION82
2.2786-2.36980.28151350.26962515X-RAY DIFFRACTION92
2.3698-2.47770.33611460.2472668X-RAY DIFFRACTION98
2.4777-2.60830.31711410.2392736X-RAY DIFFRACTION100
2.6083-2.77170.25051500.22712759X-RAY DIFFRACTION100
2.7717-2.98570.30371660.22832715X-RAY DIFFRACTION100
2.9857-3.28620.24431540.22462756X-RAY DIFFRACTION100
3.2862-3.76170.26481430.19142788X-RAY DIFFRACTION100
3.7617-4.73910.18761720.15292789X-RAY DIFFRACTION100
4.7391-66.86320.19751210.16192992X-RAY DIFFRACTION99

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