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- PDB-4b43: Bacterial translation initiation factor IF2 (1-363), apo form, do... -

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Basic information

Entry
Database: PDB / ID: 4b43
TitleBacterial translation initiation factor IF2 (1-363), apo form, double mutant K86L H130A
ComponentsTRANSLATION INITIATION FACTOR IF-2
KeywordsTRANSLATION / INITIATION / GTP HYDROLYSIS MECHANISM
Function / homology
Function and homology information


translation initiation factor activity / GTPase activity / GTP binding / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #2480 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 ...Arc Repressor Mutant, subunit A - #2480 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Translation elongation factor EFTu-like, domain 2 / 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 / Arc Repressor Mutant, subunit A / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Translation initiation factor IF-2
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsSimonetti, A. / Urzhumtsev, A. / Klaholz, B.P.
CitationJournal: To be Published
Title: Molecular Basis of GTP Hydrolysis by Bacterial Translation Initiation Factor If2
Authors: Simonetti, A. / Marzi, S. / Fabbretti, A. / Myasnikov, A.G. / Hazemann, I. / Jenner, L. / Urzhumtsev, A. / Gualerzi, C.O. / Klaholz, B.P.
History
DepositionJul 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,39313
Polymers40,1121
Non-polymers1,28112
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.787, 61.971, 162.578
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 TRANSLATION INITIATION FACTOR IF-2 / TRANSLATION INITIATION FACTOR IF2


Mass: 40111.883 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-363 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Description: DSM 579 / Plasmid: PET-30B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48515
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS K86L AND H130A

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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: 2.83 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 6 / Details: pH 6

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 34540 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.4 / % possible all: 81.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1278)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B3X

4b3x


Resolution: 1.937→49.283 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 3732 5.8 %
Rwork0.1939 --
obs0.1963 64732 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.937→49.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 32 257 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152847
X-RAY DIFFRACTIONf_angle_d1.3673852
X-RAY DIFFRACTIONf_dihedral_angle_d15.821145
X-RAY DIFFRACTIONf_chiral_restr0.083429
X-RAY DIFFRACTIONf_plane_restr0.007514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9373-1.96180.499530.4708872X-RAY DIFFRACTION38
1.9618-1.98760.33681460.31792339X-RAY DIFFRACTION100
1.9876-2.01480.31011380.28552310X-RAY DIFFRACTION100
2.0148-2.04360.31561380.27162278X-RAY DIFFRACTION100
2.0436-2.07410.28631440.25982404X-RAY DIFFRACTION100
2.0741-2.10650.31181430.24772231X-RAY DIFFRACTION100
2.1065-2.14110.25981470.2482372X-RAY DIFFRACTION100
2.1411-2.1780.24241410.25392307X-RAY DIFFRACTION100
2.178-2.21760.34391400.26052311X-RAY DIFFRACTION100
2.2176-2.26020.45731390.37582236X-RAY DIFFRACTION97
2.2602-2.30640.38021390.28322277X-RAY DIFFRACTION97
2.3064-2.35650.25991350.20912284X-RAY DIFFRACTION100
2.3565-2.41140.23811470.19532356X-RAY DIFFRACTION100
2.4114-2.47170.24761350.19822283X-RAY DIFFRACTION100
2.4717-2.53850.26671410.18882324X-RAY DIFFRACTION100
2.5385-2.61320.29131360.19452290X-RAY DIFFRACTION100
2.6132-2.69750.21861490.18682387X-RAY DIFFRACTION100
2.6975-2.79390.27941340.17872264X-RAY DIFFRACTION100
2.7939-2.90580.25761420.19442325X-RAY DIFFRACTION100
2.9058-3.0380.23991460.1962335X-RAY DIFFRACTION100
3.038-3.19810.24411410.18712308X-RAY DIFFRACTION100
3.1981-3.39850.26441410.17692314X-RAY DIFFRACTION100
3.3985-3.66080.17461470.16452336X-RAY DIFFRACTION100
3.6608-4.0290.17631390.15392310X-RAY DIFFRACTION100
4.029-4.61170.18241450.15012315X-RAY DIFFRACTION100
4.6117-5.80880.17451410.16442328X-RAY DIFFRACTION100
5.8088-49.2990.2271450.19012304X-RAY DIFFRACTION100

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