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- PDB-4tmz: Translation initiation factor eIF5B (517-858) from C. thermophilu... -

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Basic information

Entry
Database: PDB / ID: 4tmz
TitleTranslation initiation factor eIF5B (517-858) from C. thermophilum, bound to GTPgammaS and potassium
ComponentseIF5B
KeywordsTRANSLATION / Translation factor / GTPase
Function / homology
Function and homology information


protein-synthesizing GTPase / translation initiation factor activity / GTPase activity / GTP binding / mitochondrion / metal ion binding
Similarity search - Function
Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain ...Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / : / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsKuhle, B. / Ficner, R.
CitationJournal: Embo J. / Year: 2014
Title: A monovalent cation acts as structural and catalytic cofactor in translational GTPases.
Authors: Kuhle, B. / Ficner, R.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Feb 24, 2016Group: Structure summary
Revision 1.4Dec 20, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: eIF5B
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,10811
Polymers76,7402
Non-polymers1,3689
Water3,045169
1
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1367
Polymers38,3701
Non-polymers7666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9734
Polymers38,3701
Non-polymers6033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.130, 116.130, 120.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAB515 - 8452 - 332
2chain BBA515 - 8462 - 333
DetailsThe biological unit is a monomer. There are 2 fragments of the biological unit in the asymmetric unit (chains A & B)

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein eIF5B


Mass: 38370.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G domain and domain II / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0S8G9*PLUS

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Non-polymers , 6 types, 178 molecules

#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe accession number on NCBI for the corresponding gene is XP_006693439.

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, glycerol, KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 38004 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 46.06 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 0.971 / Net I/σ(I): 21.43 / Num. measured all: 307464
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.28-2.420.9070.543.8422770275927440.64699.7
2.34-2.40.9210.4884.6222242270026990.52100
2.4-2.470.9450.3955.4921036261026100.422100
2.47-2.550.9560.3166.3519131255325510.3499.9
2.55-2.630.9750.2677.8520450246324630.284100
2.63-2.730.9850.2149.620586241524150.228100
2.73-2.830.9880.17811.4419701233423340.19100
2.83-2.950.9930.13214.7118579222022200.141100
2.95-3.080.9960.09818.8317813215121510.104100
3.08-3.230.9970.07622.7516231206620650.081100
3.23-3.40.9980.05727.8914966195419540.061100
3.4-3.610.9990.0534.7215842185718570.053100
3.61-3.860.9990.04339.4914744175817580.046100
3.86-4.170.9990.03743.8613520165316520.03999.9
4.17-4.560.9990.03546.2211879151215100.03799.9
4.56-5.10.9980.03445.8110001138613860.036100
5.1-5.890.9990.03546.910135123312330.038100
5.89-7.210.9990.03347.18360106410610.03699.7
7.21-10.20.9990.03149.9758008458410.03499.5
10.20.9980.0355.7136785095000.03398.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.68 Å47.68 Å
Translation4.68 Å47.68 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE2.5.2data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1690)refinement
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCN

4ncn


Resolution: 2.28→47.679 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1901 5 %
Rwork0.1997 36098 -
obs0.2016 37999 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.45 Å2 / Biso mean: 60.7918 Å2 / Biso min: 28.21 Å2
Refinement stepCycle: final / Resolution: 2.28→47.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5151 0 76 169 5396
Biso mean--48.94 50.84 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045381
X-RAY DIFFRACTIONf_angle_d1.0227274
X-RAY DIFFRACTIONf_chiral_restr0.038828
X-RAY DIFFRACTIONf_plane_restr0.004936
X-RAY DIFFRACTIONf_dihedral_angle_d16.292069
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3058X-RAY DIFFRACTION4.679TORSIONAL
12B3058X-RAY DIFFRACTION4.679TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2813-2.33840.31651320.25942495262799
2.3384-2.40160.31811330.256625382671100
2.4016-2.47230.28591350.245625512686100
2.4723-2.55210.27811330.239925272660100
2.5521-2.64330.25191350.23825642699100
2.6433-2.74910.28251330.235425412674100
2.7491-2.87420.2891350.2425512686100
2.8742-3.02570.26061340.22225512685100
3.0257-3.21520.22581360.214925842720100
3.2152-3.46340.25711350.202825612696100
3.4634-3.81180.2311370.19526012738100
3.8118-4.36310.21881370.171226052742100
4.3631-5.49570.18331390.166926542793100
5.4957-47.68990.23981470.190427752922100
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)
17.5023-0.56271.63242.9348-0.42494.9039-0.22060.53860.54450.05910.1534-0.7326-0.16280.88040.0410.34620.03260.00050.3514-0.06670.47140.4357-31.482-13.1965
24.1008-1.6495-1.33192.8490.8931.81680.061-0.13360.80660.01140.1382-0.2968-0.27910.0194-0.13090.33310.01280.00570.2887-0.01810.4001-10.4209-26.5607-14.7584
36.7602-0.1028-1.33247.0669-0.79275.18230.08360.2428-0.0099-0.4259-0.1136-0.38380.25970.34590.01320.30950.00690.01290.3914-0.06040.32899.8118-48.8221-21.8822
46.6531-1.7587-1.61968.2666-2.22075.55140.08470.67220.4607-0.89630.2670.3629-0.0112-0.4636-0.29380.37360.01160.02180.41790.02230.46516.3132-37.6675-26.8997
57.9646-2.728-1.43147.6998-1.81365.4747-0.1095-0.95770.11050.323-0.0796-0.46570.07070.4160.09320.38790.001-0.060.4149-0.00080.432110.9705-52.688-16.3645
63.0753-1.2028-1.09775.55392.60115.06820.07820.1299-0.34910.7131-0.5032-0.03621.0206-0.59950.49410.4394-0.096-0.01160.7714-0.1160.3767-25.5606-67.1264-40.7813
73.5920.1150.50862.9681-0.33732.66940.0653-0.0723-0.05520.0597-0.18780.33220.1017-0.88660.12870.2855-0.11550.03760.7317-0.14320.3669-28.8713-58.1803-36.9435
82.08790.02980.37653.0449-1.11971.46640.12650.3213-0.0408-0.0765-0.18761.0026-0.14-1.24160.05820.4254-0.0067-0.04891.3118-0.23790.7084-43.1235-54.7139-40.8586
96.0954-0.7846-0.40783.036-0.0062.8240.0305-0.3918-0.29630.3138-0.13470.02320.2942-0.22070.09990.4933-0.12220.04810.4287-0.00250.3904-11.6269-70.2965-34.3461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 515 through 535 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 536 through 753 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 754 through 798 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 799 through 826 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 827 through 846 )B0
6X-RAY DIFFRACTION6chain 'A' and (resid 515 through 535 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 536 through 652 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 653 through 735 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 736 through 845 )A0

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