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- PDB-6rvu: Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) -

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Basic information

Entry
Database: PDB / ID: 6rvu
TitleCrystal structure of the Burkholderia Lethal Factor 1 (BLF1)
ComponentsLethal Factor 1 (BLF1)
KeywordsTOXIN / Glutamine deamidase toxin / cysteine protease / CNF1 family
Function / homologyBurkholderia lethal factor 1 / Burkholderia lethal factor 1 / symbiont-mediated suppression of host translation initiation / Uncharacterized protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.99 Å
AuthorsMobbs, G.W. / Aziz, A.A. / Blackburn, G.M. / Sedelnikova, S.E. / Minshull, T.C. / Dickman, M.J. / Baker, P.J. / Nathan, S. / Firdaus-Raih, M. / Rice, D.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Royal SocietyIC170306 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M012166/1 United Kingdom
CitationJournal: Commun Biol / Year: 2022
Title: Molecular basis of specificity and deamidation of eIF4A by Burkholderia Lethal Factor 1.
Authors: Mobbs, G.W. / Aziz, A.A. / Dix, S.R. / Blackburn, G.M. / Sedelnikova, S.E. / Minshull, T.C. / Dickman, M.J. / Baker, P.J. / Nathan, S. / Raih, M.F. / Rice, D.W.
History
DepositionJun 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lethal Factor 1 (BLF1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7805
Polymers25,5311
Non-polymers2484
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint10 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.259, 44.586, 116.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lethal Factor 1 (BLF1)


Mass: 25531.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria)
Strain: K96243 / Gene: BPSL1549 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63UP7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M potassium thiocyanate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 0.99→44.58 Å / Num. obs: 93887 / % possible obs: 86.7 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 12.6 / Num. measured all: 548111 / Scaling rejects: 651
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.99-1.021.30.279210015560.7930.2420.3721.618.6
4.33-44.586.60.075993614970.9930.0310.08122.6100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TU8

3tu8


Resolution: 0.99→41.69 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.598 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.147 4639 5 %RANDOM
Rwork0.1251 ---
obs0.1262 89039 86.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.97 Å2 / Biso mean: 13.399 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 0.99→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 20 369 2027
Biso mean--18.02 25.66 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131795
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171600
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6452444
X-RAY DIFFRACTIONr_angle_other_deg1.571.5723735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2415233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78922.93592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76715293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2641510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022065
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02385
X-RAY DIFFRACTIONr_rigid_bond_restr40.39533395
LS refinement shellResolution: 0.994→1.019 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 79 -
Rwork0.297 1325 -
all-1404 -
obs--17.71 %

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