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- PDB-6u43: Crystal structure of Methanoperedens nitroreducens elongation fac... -

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Basic information

Entry
Database: PDB / ID: 6u43
TitleCrystal structure of Methanoperedens nitroreducens elongation factor 2 H595N bound to GMPPCP and magnesium (triclinic crystal form)
ComponentsElongation factor 2
KeywordsTRANSLATION / GTPase / ribosomal translocase / elongation
Function / homology
Function and homology information


translation elongation factor activity / ribonucleoprotein complex / GTPase activity / GTP binding / metal ion binding / cytosol
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: 1.4 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 1.1Oct 11, 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
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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0776
Polymers83,3041
Non-polymers7735
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.195, 62.524, 63.396
Angle α, β, γ (deg.)64.210, 69.680, 80.510
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Elongation factor 2 / EF-2


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

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Non-polymers , 5 types, 812 molecules

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


Mass: 521.208 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.4 Å3/Da / Density % sol: 48.64 %
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: 1.4→56.3 Å / Num. obs: 131884 / % possible obs: 90.3 % / Redundancy: 2.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.7
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 17221 / CC1/2: 0.72

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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: Saccharomyces cerevisiae EF-2 (PDB entry 1N0V)

1n0v


Resolution: 1.4→54.264 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 6514 4.94 %
Rwork0.1652 125346 -
obs0.1665 131860 90.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.47 Å2 / Biso mean: 37.3984 Å2 / Biso min: 16.65 Å2
Refinement stepCycle: final / Resolution: 1.4→54.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5549 0 44 807 6400
Biso mean--45.71 49.61 -
Num. residues----723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.42931640.43273000X-RAY DIFFRACTION65
1.4159-1.43260.4291810.38783500X-RAY DIFFRACTION75
1.4326-1.450.36692210.34294066X-RAY DIFFRACTION89
1.45-1.46840.34162120.31394164X-RAY DIFFRACTION90
1.4684-1.48770.28872460.29214185X-RAY DIFFRACTION91
1.4877-1.50810.33112510.26344194X-RAY DIFFRACTION91
1.5081-1.52970.29172100.24084239X-RAY DIFFRACTION91
1.5297-1.55250.26412140.23944262X-RAY DIFFRACTION92
1.5525-1.57670.27082070.2254217X-RAY DIFFRACTION91
1.5767-1.60260.26632120.2124196X-RAY DIFFRACTION91
1.6026-1.63020.25972000.21024168X-RAY DIFFRACTION89
1.6302-1.65990.22142340.1974246X-RAY DIFFRACTION93
1.6599-1.69180.23852100.20424331X-RAY DIFFRACTION93
1.6918-1.72630.24342260.2144275X-RAY DIFFRACTION93
1.7263-1.76390.21752240.19424292X-RAY DIFFRACTION92
1.7639-1.80490.21172080.18194263X-RAY DIFFRACTION92
1.8049-1.85010.21421950.16484240X-RAY DIFFRACTION91
1.8501-1.90010.19422070.15564228X-RAY DIFFRACTION90
1.9001-1.9560.17871950.15754098X-RAY DIFFRACTION89
1.956-2.01910.18662560.15784288X-RAY DIFFRACTION94
2.0191-2.09130.18722330.16564356X-RAY DIFFRACTION94
2.0913-2.1750.1942400.14724307X-RAY DIFFRACTION94
2.175-2.2740.18122090.14574295X-RAY DIFFRACTION93
2.274-2.39390.17882330.14854234X-RAY DIFFRACTION91
2.3939-2.54390.18752060.15584105X-RAY DIFFRACTION89
2.5439-2.74030.20052420.16234401X-RAY DIFFRACTION95
2.7403-3.01610.21072600.16424309X-RAY DIFFRACTION94
3.0161-3.45240.1752100.15454223X-RAY DIFFRACTION91
3.4524-4.34940.14652150.1394316X-RAY DIFFRACTION93
4.3494-54.2640.1671930.15684348X-RAY DIFFRACTION93

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