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- PDB-4tmx: Translation initiation factor eIF5B (517-858) mutant D533N from C... -

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Basic information

Entry
Database: PDB / ID: 4tmx
TitleTranslation initiation factor eIF5B (517-858) mutant D533N from C. thermophilum, bound to GTP and sodium
ComponentseIF5B
KeywordsTRANSLATION / Translation factor / GTPase / monovalent cation / translation initiation
Function / homology
Function and homology information


protein-synthesizing GTPase / translation initiation factor activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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
A: eIF5B
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,80823
Polymers76,7382
Non-polymers2,07021
Water15,115839
1
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,37411
Polymers38,3691
Non-polymers1,00510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43412
Polymers38,3691
Non-polymers1,06511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.530, 116.820, 66.490
Angle α, β, γ (deg.)90.000, 101.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISHISGLUGLUchain AAA515 - 8562 - 343
2GLYGLYASPASPchain BBB514 - 8581 - 345
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 AB

#1: Protein eIF5B


Mass: 38369.031 Da / Num. of mol.: 2 / Fragment: G domain and domain II / Mutation: D533N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: G0S8G9*PLUS

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Non-polymers , 6 types, 860 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25 / Details: HEPES, PEG 4000, 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: 1.5→46.43 Å / Num. obs: 131458 / % possible obs: 99.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.33 Å2 / Rmerge F obs: 1 / Rrim(I) all: 0.029 / Χ2: 0.988 / Net I/σ(I): 24.4 / Num. measured all: 542891
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obs
1.5-1.590.8032.936090979394670.59898.2
1.54-1.580.8713.7739964951794820.46399.60.405
1.58-1.630.9214.7738896928092320.36299.50.316
1.63-1.680.9435.8737065899589420.28999.40.252
1.68-1.730.9637.3935447874986730.22399.10.194
1.73-1.790.9769.2331617846083210.16998.40.146
1.79-1.860.98813.1634375811480930.12299.70.107
1.86-1.940.99216.533382783678060.09799.60.085
1.94-2.020.99620.9131902751574950.07499.70.065
2.02-2.120.99727.6130407724771930.05499.30.047
2.12-2.240.99833.2426808686367770.04298.70.036
2.24-2.370.99941.7927067646164500.03399.80.029
2.37-2.540.99950.3826542610460920.02799.80.024
2.54-2.740.99956.4724149564556320.02499.80.021
2.74-30.99964.5121703524352010.0299.20.018
3-3.35178.9617627472846480.01598.30.013
3.35-3.871104.0217990417541720.01299.90.01
3.87-4.74112214927355135390.0199.70.009
4.74-6.711104.7710235274627170.01198.90.01
6.711119.586698153115230.01499.50.012

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.55 Å46.43 Å
Translation4.55 Å46.43 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: 1.5→46.43 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1816 6573 5 %
Rwork0.155 124875 -
obs0.1564 131448 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.44 Å2 / Biso mean: 25.4756 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.5→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 128 880 6365
Biso mean--25.27 37 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146060
X-RAY DIFFRACTIONf_angle_d1.6198235
X-RAY DIFFRACTIONf_chiral_restr0.086917
X-RAY DIFFRACTIONf_plane_restr0.0091094
X-RAY DIFFRACTIONf_dihedral_angle_d17.5842368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3202X-RAY DIFFRACTION8.58TORSIONAL
12B3202X-RAY DIFFRACTION8.58TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5004-1.51740.29352040.25393883408794
1.5174-1.53530.25442200.23014183440399
1.5353-1.5540.2432180.214341364354100
1.554-1.57370.23252200.208941714391100
1.5737-1.59440.23312200.199441974417100
1.5944-1.61620.21582200.19674164438499
1.6162-1.63930.24232180.18814146436499
1.6393-1.66380.21442180.1854152437099
1.6638-1.68980.22062200.179241664386100
1.6898-1.71750.23652170.1744137435499
1.7175-1.74710.19282210.17834183440499
1.7471-1.77890.19642140.17814076429098
1.7789-1.81310.21052200.17214176439699
1.8131-1.85010.18162220.160142144436100
1.8501-1.89040.18732170.1641224339100
1.8904-1.93430.19492180.159241514369100
1.9343-1.98270.19672220.159342194441100
1.9827-2.03630.18742190.155741574376100
2.0363-2.09620.17632210.15154192441399
2.0962-2.16390.17852180.14984149436799
2.1639-2.24120.17512190.14954153437299
2.2412-2.3310.17632190.145641604379100
2.331-2.4370.16782220.14542264448100
2.437-2.56550.1882200.147741744394100
2.5655-2.72620.18322200.153241774397100
2.7262-2.93670.19232200.15454198441899
2.9367-3.23220.16432180.14964134435298
3.2322-3.69970.1692230.143742284451100
3.6997-4.66050.15012210.129842154436100
4.6605-46.45220.17272240.15744236446099
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)
11.04530.1281-0.1411.45610.01320.90190.0078-0.07510.040.09220.01330.0079-0.0267-0.0089-0.01930.1048-0.01160.00580.1095-0.00930.078351.555821.615320.7107
21.2787-0.2548-0.20443.42160.88581.1710.0090.0215-0.1740.02330.0021-0.18470.083-0.03350.01220.15530.01080.00240.2249-0.0040.208767.7933-0.313216.7351
31.8034-0.6803-0.22155.1248-0.02531.18730.06420.0974-0.089-0.36020.01460.05950.0119-0.0755-0.05310.15420.00170.01470.2087-0.02460.169865.4214.42099.9074
45.835-3.1941.52828.4016-0.92796.1780.4286-1.1909-1.24440.90680.03650.07651.134-0.2401-0.40950.5171-0.0821-0.10810.48460.08570.485673.5927-10.213924.37
51.1179-0.04550.01081.4510.4251.54270.0083-0.0473-0.0080.0484-0.0413-0.00130.0091-0.00470.03030.10140.0086-0.01010.1160.00510.127939.1619-13.3621.7136
61.3797-0.2044-0.38013.1836-0.06533.0170.05710.1217-0.2728-0.0941-0.1480.26870.1685-0.24220.06420.08170.0324-0.0310.1288-0.02710.15730.6361-14.316-6.8738
71.961-0.39721.07892.77190.03843.3974-0.04110.1130.3157-0.1793-0.0499-0.0321-0.45810.10610.10680.2154-0.01580.00030.10110.02140.184840.19977.7777-7.0885
85.00665.3749-0.81028.1586-1.63972.038-0.11560.35370.4535-0.53610.04340.6638-0.2665-0.2240.06680.23850.0801-0.07030.22620.00970.179328.6897-0.6079-15.8703
90.9536-0.1091-0.19991.5976-0.21242.3680.01890.03950.0298-0.0662-0.00680.3483-0.1137-0.3836-0.00230.12950.0282-0.02420.1525-0.02020.184729.8705-3.7306-1.2995
105.7705-2.6972-0.63013.83540.20352.67510.0396-0.0925-0.0213-0.02180.0008-0.12040.13980.17750.00520.1227-0.0339-0.01030.11840.02340.105839.0527-24.376210.4915
112.2720.7470.20192.9957-0.60852.40310.0278-0.0129-0.187-0.0609-0.0834-0.32960.29630.13720.05010.18040.0165-0.02220.16450.03780.139547.3381-27.549213.5562
122.89680.4448-0.35044.4102-1.41727.113-0.0709-0.0896-0.5281-0.2952-0.00230.38211.3203-0.98430.09210.4766-0.1085-0.02370.3110.0020.298538.3727-39.919713.1038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 515 through 736 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 737 through 797 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 798 through 838 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 839 through 856 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 514 through 626 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 627 through 652 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 653 through 672 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 673 through 693 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 694 through 736 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 737 through 771 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 772 through 826 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 827 through 858 )B0

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