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- PDB-1vb5: Crystal Structure Analysis of the Pyrococcus horikoshii OT3 trans... -

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Basic information

Entry
Database: PDB / ID: 1vb5
TitleCrystal Structure Analysis of the Pyrococcus horikoshii OT3 translation initiation factor eIF-2B
Componentstranslation initiation factor eIF-2B
KeywordsTRANSLATION / initiation factor
Function / homology
Function and homology information


translation initiation factor activity / guanyl-nucleotide exchange factor activity
Similarity search - Function
translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Putative translation initiation factor eIF-2B subunit 2-like
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsKakuta, Y. / Tahara, M. / Maetani, S. / Kimura, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyperthermophilic archaeon Pyrococcus horikoshii OT3: a proposed structure of the regulatory subcomplex of eukaryotic IF2B
Authors: Kakuta, Y. / Tahara, M. / Maetani, S. / Yao, M. / Tanaka, I. / Kimura, M.
History
DepositionFeb 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: translation initiation factor eIF-2B
B: translation initiation factor eIF-2B


Theoretical massNumber of molelcules
Total (without water)62,8892
Polymers62,8892
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-19 kcal/mol
Surface area22920 Å2
MethodPISA
2
A: translation initiation factor eIF-2B
B: translation initiation factor eIF-2B

A: translation initiation factor eIF-2B
B: translation initiation factor eIF-2B


Theoretical massNumber of molelcules
Total (without water)125,7784
Polymers125,7784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area10250 Å2
ΔGint-38 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.437, 158.437, 151.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein translation initiation factor eIF-2B


Mass: 31444.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Production host: Escherichia coli (E. coli) / References: GenBank: 14590355, UniProt: O58185*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.36 Å3/Da / Density % sol: 71.81 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 58196

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å /
RfactorNum. reflection
Rfree0.234 -
Rwork0.209 -
obs-51978
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 0 208 4594

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