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- PDB-4tmt: Translation initiation factor eIF5B (517-858) mutant D533A from C... -

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Basic information

Entry
Database: PDB / ID: 4tmt
TitleTranslation initiation factor eIF5B (517-858) mutant D533A from C. thermophilum, bound to GTPgammaS
ComponentseIF5B
KeywordsTRANSLATION / Translation factor / Initiation / GTPase / Monovalent cation
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 domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type 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 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
ACETIC ACID / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 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: 1.58 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 1.2Feb 24, 2016Group: Structure summary
Revision 1.3Dec 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)78,80922
Polymers76,6522
Non-polymers2,15720
Water13,025723
1
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,39010
Polymers38,3261
Non-polymers1,0649
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,42012
Polymers38,3261
Non-polymers1,09411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-24 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.410, 115.910, 66.090
Angle α, β, γ (deg.)90.000, 101.370, 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
1METMETSERSERchain AAA516 - 8573 - 344
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: 38326.008 Da / Num. of mol.: 2 / Fragment: G domain and domain II / Mutation: D533A
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 , 7 types, 743 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / 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: 1.58→46.37 Å / Num. obs: 110416 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.58 Å2 / Net I/σ(I): 17.7
Reflection shellResolution: 1.58→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) all: 2.23 / Rejects: 0 / % possible all: 98

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.56 Å46.37 Å
Translation4.56 Å46.37 Å

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Processing

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

4ncn


Resolution: 1.58→46.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.23 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 5521 5 %
Rwork0.1687 104883 -
obs0.1699 110404 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.98 Å2 / Biso mean: 25.7204 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 1.58→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5343 0 128 760 6231
Biso mean--28.13 38.38 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125774
X-RAY DIFFRACTIONf_angle_d1.4637815
X-RAY DIFFRACTIONf_chiral_restr0.07886
X-RAY DIFFRACTIONf_plane_restr0.0071018
X-RAY DIFFRACTIONf_dihedral_angle_d14.2942225
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3162X-RAY DIFFRACTION6.423TORSIONAL
12B3162X-RAY DIFFRACTION6.423TORSIONAL
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 (%)
1.5799-1.59790.26861760.25743338351496
1.5979-1.61670.30121860.24483543372999
1.6167-1.63640.23461820.23423449363199
1.6364-1.65710.25451830.23753486366999
1.6571-1.67890.281880.22413560374899
1.6789-1.70190.23441800.21413431361199
1.7019-1.72620.24991860.20533526371299
1.7262-1.7520.24871820.20493462364499
1.752-1.77940.24381860.21283540372699
1.7794-1.80860.2711820.20673443362599
1.8086-1.83970.21771860.184435333719100
1.8397-1.87320.21281820.17353471365399
1.8732-1.90920.19541870.17163549373699
1.9092-1.94820.20261830.169434793662100
1.9482-1.99060.1931860.165635293715100
1.9906-2.03690.18621830.15693470365399
2.0369-2.08780.19831850.16333527371299
2.0878-2.14430.19191860.16643540372699
2.1443-2.20740.18511820.15753457363998
2.2074-2.27860.19151830.16033479366298
2.2786-2.360.17881850.15873515370099
2.36-2.45450.18141830.16033460364399
2.4545-2.56620.20461860.16853538372499
2.5662-2.70150.22111850.17163511369699
2.7015-2.87070.18611840.16673510369499
2.8707-3.09240.18711850.16073512369799
3.0924-3.40350.17221810.15293430361198
3.4035-3.89570.17191860.15183539372599
3.8957-4.90740.16771840.14493494367899
4.9074-46.39020.18431880.18643562375099
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)
11.2319-0.12170.03141.34650.29861.1276-0.04-0.04080.00240.0186-0.00350.06340.0244-0.0580.04550.1159-0.017400.10040.00250.0891-4.452822.057420.6884
20.7354-0.24870.03622.47390.31350.46040.03440.0808-0.038-0.1598-0.0466-0.0728-0.0029-0.08390.00430.17570.02360.0230.232-0.00550.184211.44932.770813.9325
34.3141-1.50021.63821.1224-0.28241.22020.0501-0.9442-0.3230.40490.1481-0.05410.3656-0.0962-0.16620.2687-0.01910.01130.40450.0070.251313.6842-9.370220.9877
40.9143-0.07430.03281.1028-0.05790.9671-0.00680.03580.0403-0.0389-0.02720.0767-0.0425-0.06590.02490.10240.003-0.00210.1283-0.01970.1279-20.4267-8.4382-1.9753
52.56760.08340.15362.8217-0.2432.5718-0.02870.0183-0.1495-0.041-0.0612-0.31510.23030.21660.0870.14130.00980.00870.14740.01790.1232-7.4467-27.684912.0833
63.1916-0.59130.3622.2087-0.00694.3225-0.17010.0066-0.4816-0.2173-0.00080.15240.8886-0.95360.13940.4167-0.13050.01520.3045-0.03450.2512-16.9913-39.4312.2335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 516 through 736 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 737 through 826 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 827 through 857 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 514 through 753 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 754 through 826 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 827 through 858 )B0

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