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- PDB-1x6o: Structural Analysis of Leishmania braziliensis eukaryotic initiat... -

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Basic information

Entry
Database: PDB / ID: 1x6o
TitleStructural Analysis of Leishmania braziliensis eukaryotic initiation factor 5a
Componentseukaryotic initiation factor 5a
KeywordsTRANSLATION / SGPP / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / translation initiation factor activity / ribosome binding
Similarity search - Function
Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Eukaryotic translation initiation factor 5A
Similarity search - Component
Biological speciesLeishmania braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsBosch, J. / Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Structural Analysis of Leishmania braziliensis eukaryotic initiation factor 5a
Authors: Bosch, J. / Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium
History
DepositionAug 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AT THE TIME OF PROCESSING THERE WAS NO SUITABLE SEQUENCE DATABASE REFERENCE FOR THIS PROTIEN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eukaryotic initiation factor 5a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9702
Polymers18,8641
Non-polymers1061
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.991, 64.991, 88.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-3802-

PEG

21A-3813-

HOH

31A-4017-

HOH

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Components

#1: Protein eukaryotic initiation factor 5a


Mass: 18863.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: A4HE05
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG 400, Potassium thiocyanate, Sodium Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-210.979251
SYNCHROTRONSSRL BL9-120.9791,0.8434,0.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 12, 2004
ADSC QUANTUM 3152CCDJun 13, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792511
20.97911
30.84341
40.97931
ReflectionResolution: 1.6→44 Å / Num. obs: 28757 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 19.523 Å2 / Rsym value: 0.048 / Net I/σ(I): 12.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 4184 / Rsym value: 0.386 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.762 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Isotropic with TLS (2 TLS groups per monomer)
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Seleno MAD used to solve higher resolution crystal, rigid body fit of MAD model was refined against native data
RfactorNum. reflection% reflectionSelection details
Rfree0.21398 1460 5.1 %RANDOM
Rwork0.17444 ---
all0.1765 ---
obs0.1765 27121 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 7 325 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9761484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15426.36444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50915181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.228153
X-RAY DIFFRACTIONr_chiral_restr0.1310.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2463
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.4814724
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.56461155
X-RAY DIFFRACTIONr_scbond_it4.4826399
X-RAY DIFFRACTIONr_scangle_it6.68310329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.684 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.265 216
Rwork0.223 3852
obs-3852
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7619-0.1285-0.34331.9177-1.50643.69150.04370.0070.0003-0.00760.03210.0090.2114-0.0524-0.0758-0.2357-0.0029-0.0122-0.2277-0.0027-0.246553.959210.030921.4019
24.7867-2.7131.99223.6145-2.1334.21840.16680.16130.0665-0.1923-0.2794-0.21270.10450.37910.1127-0.21690.03230.0121-0.18320.0311-0.214243.110530.23485.1101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 5127 - 59
2X-RAY DIFFRACTION1AA56 - 8664 - 94
3X-RAY DIFFRACTION2AA87 - 16495 - 172

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