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- PDB-5k34: Structure of the ankyrin domain of AnkB from Legionella Pneumophila -

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Basic information

Entry
Database: PDB / ID: 5k34
TitleStructure of the ankyrin domain of AnkB from Legionella Pneumophila
ComponentsAnkyrin-repeat protein B
KeywordsPROTEIN BINDING / bacterial effector / ankyrin domain / protein-protein interaction / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologyF-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / Ankyrin repeats (3 copies) / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ankyrin-repeat protein B / F-box protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsWong, K. / Kozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: Structure / Year: 2017
Title: Structural Mimicry by a Bacterial F Box Effector Hijacks the Host Ubiquitin-Proteasome System.
Authors: Wong, K. / Perpich, J.D. / Kozlov, G. / Cygler, M. / Abu Kwaik, Y. / Gehring, K.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ankyrin-repeat protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9573
Polymers13,7691
Non-polymers1882
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-7 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.322, 80.485, 54.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-339-

HOH

31A-403-

HOH

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Components

#1: Protein Ankyrin-repeat protein B


Mass: 13768.890 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: ankB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0A1EKG3, UniProt: Q5ZTL7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M HEPES pH 7.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 39731 / % possible obs: 98.6 % / Redundancy: 3.6 % / Rsym value: 0.104 / Net I/σ(I): 22.3
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→45.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.264 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 2113 5 %RANDOM
Rwork0.17303 ---
obs0.17395 39731 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.69 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.15→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 11 166 1093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9831312
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88624.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45215196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.036156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021713
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.025461
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7351.532577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4361.406510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined1.20510.7121717
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.4933971
X-RAY DIFFRACTIONr_sphericity_free6.985540
X-RAY DIFFRACTIONr_sphericity_bonded3.19151078
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 157 -
Rwork0.224 2863 -
obs--97.61 %

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