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- PDB-3pen: Structure of archaeal initiation factor aIF2gamma subunit delta 3... -

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Basic information

Entry
Database: PDB / ID: 3pen
TitleStructure of archaeal initiation factor aIF2gamma subunit delta 37-47 from Sulfolobus solfataricus in the GDP-bound form.
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsRNA BINDING PROTEIN / RNA / Met / Archaeal Proteins / Binding Sites / Prokaryotic Init Factor-2 / Guanosine Diphosphate
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 ...Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3005 Å
AuthorsArkhipova, V.I. / Lazopulo, A.M. / Lazopulo, S.M. / Garber, M.B. / Nikonov, O.S. / Nikonov, S.V. / Gabdoulkhakov, A.G.
CitationJournal: TO BE PUBLISHED
Title: Structure of archaeal initiation factor aIF2gamma subunit from Sulfolobus solfataricus in the GDP-bound form.
Authors: Arkhipova, V.I. / Lazopulo, A.M. / Lazopulo, S.M. / Garber, M.B. / Nikonov, O.S. / Nikonov, S.V. / Gabdoulkhakov, A.G.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3608
Polymers44,4331
Non-polymers9287
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.120, 187.120, 187.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Translation initiation factor 2 subunit gamma / aIF2-gamma / eIF-2-gamma


Mass: 44432.547 Da / Num. of mol.: 1 / Mutation: deletion UNP residues 37-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g, SSO0412 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q980A5
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 6.14 Å3/Da / Density % sol: 79.9 %
Crystal growTemperature: 301 K / pH: 6.5
Details: 1.6M Sodium formate, 44mM Sodium cacodylate, GDPNP, GDP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 192.6 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2010 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 48144 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.88
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.42 / % possible all: 83

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PMD

2pmd


Resolution: 2.3005→19.1 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2407 5 %
Rwork0.19 --
obs0.191 48144 99.9 %
all-48206 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.12 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3005→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 57 313 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083239
X-RAY DIFFRACTIONf_angle_d1.2874398
X-RAY DIFFRACTIONf_dihedral_angle_d20.7711210
X-RAY DIFFRACTIONf_chiral_restr0.095513
X-RAY DIFFRACTIONf_plane_restr0.004547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3005-2.34740.30631410.27452672X-RAY DIFFRACTION100
2.3474-2.39830.27631400.2552668X-RAY DIFFRACTION100
2.3983-2.4540.30751400.24772664X-RAY DIFFRACTION100
2.454-2.51520.25181400.23522665X-RAY DIFFRACTION100
2.5152-2.58310.26951420.23252682X-RAY DIFFRACTION100
2.5831-2.65890.25511400.23242668X-RAY DIFFRACTION100
2.6589-2.74450.26641420.23032688X-RAY DIFFRACTION100
2.7445-2.84230.29981400.2232672X-RAY DIFFRACTION100
2.8423-2.95570.26021420.22362705X-RAY DIFFRACTION100
2.9557-3.08970.22491400.21722657X-RAY DIFFRACTION100
3.0897-3.25180.24021420.19972685X-RAY DIFFRACTION100
3.2518-3.45440.1921410.17612686X-RAY DIFFRACTION100
3.4544-3.71930.18771420.16272699X-RAY DIFFRACTION100
3.7193-4.09030.17861420.14742697X-RAY DIFFRACTION100
4.0903-4.67460.15141420.13682703X-RAY DIFFRACTION100
4.6746-5.86110.19941440.14842734X-RAY DIFFRACTION100
5.8611-19.09850.17041470.16852792X-RAY DIFFRACTION100

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