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- PDB-4tn1: Translation initiation factor eIF5B (517-858) mutant D533R from C... -

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Basic information

Entry
Database: PDB / ID: 4tn1
TitleTranslation initiation factor eIF5B (517-858) mutant D533R from C. thermophilum, bound to GTPgammaS
ComponentseIF5B
KeywordsTRANSLATION / Translation factor / GTPase / Initiation / Ribosome
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: 2.75 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 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5Dec 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)77,9516
Polymers76,8242
Non-polymers1,1274
Water86548
1
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9763
Polymers38,4121
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9763
Polymers38,4121
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.690, 115.690, 119.800
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 / End auth comp-ID: ASP / End label comp-ID: ASP

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETchain AAB516 - 8453 - 332
2ASNASNchain BBA517 - 8464 - 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

#1: Protein eIF5B


Mass: 38412.121 Da / Num. of mol.: 2 / Mutation: D533R
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: MES, PEG 8000, NaOAc

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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: 2.75→50 Å / Num. obs: 21704 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 58.35 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.076 / Χ2: 1.009 / Net I/σ(I): 19.35 / Num. measured all: 154138
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
2.75-2.920.8320.5683.110900159115610.71399.1
2.82-2.90.890.4794.2910505152315230.519100
2.9-2.980.9350.4015.4210807149014900.432100
2.98-3.070.9640.3047.0811044146014600.326100
3.07-3.180.970.2448.7110561140214020.262100
3.18-3.290.9830.18810.9910147136913690.203100
3.29-3.410.9910.14413.669670133613360.155100
3.41-3.550.9930.11316.368602125712570.123100
3.55-3.710.9960.09319.388841123712370.1100
3.71-3.890.9970.07524.178643117211720.081100
3.89-4.10.9980.06128.28132111911190.066100
4.1-4.350.9990.05132.727589105710570.055100
4.35-4.650.9990.04137.746700101110110.044100
4.65-5.020.9990.03742.364919429420.04100
5.02-5.50.9990.04338.1163408778770.046100
5.5-6.150.9990.04237.3655867897890.045100
6.15-7.10.9990.03838.4244967057040.04299.9
7.1-8.710.02656.3442736176170.028100
8.7-12.310.01871.7531374904900.02100
12.310.01674.916743002910.01897

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.7 Å47.5 Å
Translation4.7 Å47.5 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: 2.75→47.498 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1085 5 %
Rwork0.2058 20615 -
obs0.2083 21700 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.19 Å2 / Biso mean: 64.4831 Å2 / Biso min: 21.37 Å2
Refinement stepCycle: final / Resolution: 2.75→47.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 66 48 5243
Biso mean--50.79 53.45 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055302
X-RAY DIFFRACTIONf_angle_d1.0317164
X-RAY DIFFRACTIONf_chiral_restr0.04820
X-RAY DIFFRACTIONf_plane_restr0.005919
X-RAY DIFFRACTIONf_dihedral_angle_d16.372028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3062X-RAY DIFFRACTION4.093TORSIONAL
12B3062X-RAY DIFFRACTION4.093TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.87510.37631320.28982495262799
2.8751-3.02670.37561320.267725382670100
3.0267-3.21630.29911340.247425332667100
3.2163-3.46450.29541330.234325382671100
3.4645-3.8130.26291350.202725612696100
3.813-4.36450.23681360.18225752711100
4.3645-5.49750.21781380.170426222760100
5.4975-47.5050.2271450.200127532898100
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)
15.65421.2342.90981.51440.41522.2547-0.46610.9380.92250.00820.3315-0.33210.21280.6281-0.19690.32170.0608-0.06040.3858-0.06370.429-1.5648-31.7505-14.8006
24.8743-1.437-0.93062.00410.80521.54070.035-0.26561.00780.13510.1252-0.346-0.3268-0.0525-0.12710.46030.02690.04450.2917-0.03580.5654-10.2789-26.0972-14.8406
33.17070.071-0.82964.4719-1.35462.38580.0610.09150.0596-0.16290.1528-0.3166-0.1352-0.0908-0.20670.3684-0.0164-0.00080.3338-0.0360.31439.1821-45.7542-22.336
41.42050.23480.0151.08460.46882.40330.10930.2559-0.1032-0.04-0.45080.47970.31-0.18540.02760.2657-0.02670.00280.762-0.15420.3649-25.74-64.1395-39.3854
52.37690.29670.36582.0076-0.27311.2589-0.07460.08620.1008-0.07040-0.0472-0.0384-0.59810.1040.2802-0.13750.02580.7339-0.07260.3344-28.8547-57.9595-36.7583
61.63890.7954-0.03421.1215-0.00630.97130.12560.45070.1278-0.1351-0.29810.664-0.2241-1.21070.17020.391-0.0191-0.02961.3015-0.15620.5891-43.0432-54.5461-40.7057
73.61661.24961.55751.97880.35851.74970.172-0.122-0.6854-0.08240.0662-0.40810.4612-0.44070.13550.4531-0.13410.10250.56630.01560.3298-18.7314-69.5017-42.7757
83.9426-0.4907-1.05322.9381-0.19292.48470.1191-0.4833-0.09270.1564-0.1165-0.060.2077-0.0701-0.03440.4022-0.12410.00740.45620.01280.3849-9.2406-70.443-31.8495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 517 through 535 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 536 through 753 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 754 through 846 )B0
4X-RAY DIFFRACTION4chain 'A' and (resid 516 through 535 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 536 through 652 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 653 through 735 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 736 through 757 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 758 through 845 )A0

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