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- PDB-6u44: Crystal structure of Methanoperedens nitroreducens elongation fac... -

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Basic information

Entry
Database: PDB / ID: 6u44
TitleCrystal structure of Methanoperedens nitroreducens elongation factor 2 H595N bound to GMPPCP and magnesium (monoclinic crystal form)
ComponentsElongation factor 2EEF2
KeywordsTRANSLATION / GTPase / ribosomal translocase / elongation
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like ...Translation elongation factor EFG/EF2, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / 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 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Elongation factor 2
Similarity search - Component
Biological speciesCandidatus Methanoperedens nitroreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFenwick, M.K. / Ealick, S.E.
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Structural basis of elongation factor 2 switching
Authors: Fenwick, M.K. / Ealick, S.E.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,41816
Polymers166,6082
Non-polymers1,80914
Water14,952830
1
A: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2098
Polymers83,3041
Non-polymers9057
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2098
Polymers83,3041
Non-polymers9057
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.322, 106.814, 98.056
Angle α, β, γ (deg.)90.000, 105.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 83304.219 Da / Num. of mol.: 2 / Mutation: H595N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanoperedens nitroreducens (archaea)
Gene: fusA, ANME2D_00299 / Plasmid: pET-DUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A062V290

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Non-polymers , 5 types, 844 molecules

#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, pH 7.1-7.6, 200 mM ammonium sulfate, 5-15 % (v/v) isopropanol, 16.5-20 % (w/v) polyethylene glycol (PEG) 4000, 9 mM GppCp, and 15 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→94.5 Å / Num. obs: 89195 / % possible obs: 98.4 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12665 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanoperedens nitroreducens elongation factor 2 H595N (triclinic crystal form)

Resolution: 2.1→75.487 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.92
RfactorNum. reflection% reflection
Rfree0.2403 4382 4.92 %
Rwork0.1866 --
obs0.1893 89111 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.7 Å2 / Biso mean: 45.7401 Å2 / Biso min: 17.36 Å2
Refinement stepCycle: final / Resolution: 2.1→75.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10805 0 100 830 11735
Biso mean--50.7 49.48 -
Num. residues----1430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.3441460.30732594X-RAY DIFFRACTION91
2.1239-2.14890.33871530.2792666X-RAY DIFFRACTION94
2.1489-2.17510.32491290.2672882X-RAY DIFFRACTION98
2.1751-2.20260.29681460.25552825X-RAY DIFFRACTION99
2.2026-2.23160.3411570.24062850X-RAY DIFFRACTION99
2.2316-2.26220.27331340.23832790X-RAY DIFFRACTION99
2.2622-2.29450.31231300.23032893X-RAY DIFFRACTION99
2.2945-2.32870.30581600.2192845X-RAY DIFFRACTION100
2.3287-2.36510.29181530.21642852X-RAY DIFFRACTION99
2.3651-2.40390.25551320.20692832X-RAY DIFFRACTION99
2.4039-2.44540.31191410.2142875X-RAY DIFFRACTION99
2.4454-2.48980.27781590.20852814X-RAY DIFFRACTION99
2.4898-2.53770.29541560.20242795X-RAY DIFFRACTION98
2.5377-2.58950.25631520.19612844X-RAY DIFFRACTION99
2.5895-2.64580.31771590.19572860X-RAY DIFFRACTION99
2.6458-2.70740.2571370.19312851X-RAY DIFFRACTION99
2.7074-2.77510.25971360.19722831X-RAY DIFFRACTION99
2.7751-2.85010.26561370.20092840X-RAY DIFFRACTION99
2.8501-2.9340.28011450.20842865X-RAY DIFFRACTION99
2.934-3.02870.24951480.20232819X-RAY DIFFRACTION98
3.0287-3.1370.24581400.18932817X-RAY DIFFRACTION98
3.137-3.26260.24661650.18282859X-RAY DIFFRACTION99
3.2626-3.4110.2431630.17252821X-RAY DIFFRACTION99
3.411-3.59090.19581380.16242832X-RAY DIFFRACTION98
3.5909-3.81580.21651460.15862835X-RAY DIFFRACTION98
3.8158-4.11040.17651540.14792790X-RAY DIFFRACTION97
4.1104-4.52410.20581340.13712853X-RAY DIFFRACTION99
4.5241-5.17860.18261340.15032864X-RAY DIFFRACTION98
5.1786-6.52390.24111500.19682796X-RAY DIFFRACTION96
6.5239-75.4870.21461480.20432839X-RAY DIFFRACTION96
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)
13.2288-1.06610.77531.2106-0.19180.8566-0.1391-0.799-0.17190.19730.25560.048-0.0117-0.1411-0.0840.29660.0362-0.00380.38690.05050.229824.724853.128235.8691
20.8465-0.12510.31052.88730.16980.8778-0.0084-0.1719-0.1166-0.0370.18910.1002-0.0924-0.1289-0.17740.22810.05650.00150.39720.02280.207330.210731.954310.96
31.63320.41110.24390.9713-0.03331.1633-0.03220.171-0.0621-0.04060.0667-0.0088-0.02110.0421-0.03550.2241-0.0064-0.00490.2251-0.01580.211166.97750.964359.8833
40.8018-0.16920.17882.8226-0.23940.9309-0.0008-0.0171-0.06410.06350.1417-0.0454-0.0952-0.0725-0.140.191-0.0227-0.02140.37170.03410.185360.772733.061983.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 437 )A7 - 437
2X-RAY DIFFRACTION2chain 'A' and (resid 438 through 728 )A438 - 728
3X-RAY DIFFRACTION3chain 'B' and (resid 7 through 437 )B7 - 437
4X-RAY DIFFRACTION4chain 'B' and (resid 438 through 728 )B438 - 728

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