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- PDB-3tua: Crystal Structure of the Burkholderia Lethal Factor 1 (BLF1) C94S... -

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Basic information

Entry
Database: PDB / ID: 3tua
TitleCrystal Structure of the Burkholderia Lethal Factor 1 (BLF1) C94S mutant
ComponentsBurkholderia Lethal Factor 1 (BLF1)
KeywordsUNKNOWN FUNCTION / toxin
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 / Resolution: 1.09 Å
AuthorsCruz, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Chang, C.T. / Mahadi, N.M. / Mobbs, G.W. / Mohamed, R. / Nathan, S. / Partridge, L.J. ...Cruz, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Chang, C.T. / Mahadi, N.M. / Mobbs, G.W. / Mohamed, R. / Nathan, S. / Partridge, L.J. / Raih, M.F. / Ruzheinikov, S.N. / Sedelnikova, S.E. / Wilson, S.A. / Rice, D.W.
Citation
Journal: Science / Year: 2011
Title: A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A.
Authors: Cruz-Migoni, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Bokori-Brown, M. / Chang, C.T. / Dickman, M.J. / Essex-Lopresti, A. / Harding, S.V. / Mahadi, N.M. / Marshall, L.E. / ...Authors: Cruz-Migoni, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Bokori-Brown, M. / Chang, C.T. / Dickman, M.J. / Essex-Lopresti, A. / Harding, S.V. / Mahadi, N.M. / Marshall, L.E. / Mobbs, G.W. / Mohamed, R. / Nathan, S. / Ngugi, S.A. / Ong, C. / Ooi, W.F. / Partridge, L.J. / Phillips, H.L. / Raih, M.F. / Ruzheinikov, S. / Sarkar-Tyson, M. / Sedelnikova, S.E. / Smither, S.J. / Tan, P. / Titball, R.W. / Wilson, S.A. / Rice, D.W.
#1: Journal: To be Published
Title: Cloning, purification and crystallographic analysis of a hypothetical protein, BPSL1549, from Burkholderia pseudomallei
Authors: Cruz-Migoni, A. / Ruzheinikov, S.N. / Sedelnikova, S.E. / Obeng, B. / Chieng, S. / Mohamed, R. / Nathan, S. / Baker, P.J. / Rice, D.W.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Burkholderia Lethal Factor 1 (BLF1)


Theoretical massNumber of molelcules
Total (without water)23,2131
Polymers23,2131
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.970, 45.220, 115.690
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 Burkholderia Lethal Factor 1 (BLF1)


Mass: 23212.715 Da / Num. of mol.: 1 / Mutation: C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSL1549 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63UP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 3350, 0.2M Sodium bromide, 0.1M bis-tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2009
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.09→37 Å / Num. all: 81372 / Num. obs: 77711 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 15
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.4 / % possible all: 75.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TU8

3tu8


Resolution: 1.09→37 Å / Num. parameters: 18544 / Num. restraintsaints: 24324 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3889 -RANDOM
Rwork0.141 ---
all0.141 73637 --
obs0.141 73637 90.5 %-
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 1555.5 / Occupancy sum non hydrogen: 1932
Refinement stepCycle: LAST / Resolution: 1.09→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 294 1932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0324
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.103

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