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- PDB-1g61: CRYSTAL STRUCTURE OF M.JANNASCHII EIF6 -

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Basic information

Entry
Database: PDB / ID: 1g61
TitleCRYSTAL STRUCTURE OF M.JANNASCHII EIF6
ComponentsTRANSLATION INITIATION FACTOR 6
KeywordsTRANSLATION / alpha-beta-barrel velcro closure subdomain / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


maturation of 5.8S rRNA / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosome binding / cytosol
Similarity search - Function
L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 6
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsGroft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of ribosome anti-association factor IF6.
Authors: Groft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 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: TRANSLATION INITIATION FACTOR 6
B: TRANSLATION INITIATION FACTOR 6


Theoretical massNumber of molelcules
Total (without water)48,9622
Polymers48,9622
Non-polymers00
Water12,683704
1
A: TRANSLATION INITIATION FACTOR 6


Theoretical massNumber of molelcules
Total (without water)24,4811
Polymers24,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSLATION INITIATION FACTOR 6


Theoretical massNumber of molelcules
Total (without water)24,4811
Polymers24,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.067, 46.964, 84.607
Angle α, β, γ (deg.)90.00, 98.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRANSLATION INITIATION FACTOR 6 / EIF-6


Mass: 24481.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0048 / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q60357
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 31% PEG-MME 2000, 0.200M Ammonium sulfate, 0.100M MES pH 5.6, 3mM Xylitol, 10mM glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
131 %(w/v)PEG2000 MME1reservoir
2100 mMMES1reservoirpH5.6
3200 mMammonium sulfate1reservoir
43 mMxylitol1reservoir
510 %(v/v)glycerol1reservoir
61 mMTCEP1reservoir
73.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.91825 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2000
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91825 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. all: 110636 / Num. obs: 110636 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 34
Reflection shellResolution: 1.3→25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.6 / Num. unique all: 20604 / % possible all: 93
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 25 Å / Num. measured all: 463351
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameClassification
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→25 Å / σ(F): 4 / σ(I): 0 / Stereochemistry target values: CNS defined library
Details: the following residue side chains were flagged during the last round of SHELX refinement as having parameters which disagree with the restraints: 2003, 2024, 4006, 4010, 4099
RfactorNum. reflection% reflectionSelection details
Rfree0.179 11040 -Random
Rwork0.132 ---
obs0.132 110239 94 %-
all-110239 --
Refinement stepCycle: LAST / Resolution: 1.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 704 4090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.3→25 Å /
Rfactor% reflection
Rfree0.179 -
Rwork0.132 -
obs-95 %
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 25 Å / σ(F): 4 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_deg2.1

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